Evarist Planet
| Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/phenoTest |
| git_branch: devel |
| git_last_commit: 689f101 |
| git_last_commit_date: 2024-10-29 09:35:40 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:47 -0500 (Tue, 24 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
| 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 1533/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| phenoTest 1.55.0 (landing page) Evarist Planet
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: phenoTest |
| Version: 1.55.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:phenoTest.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings phenoTest_1.55.0.tar.gz |
| StartedAt: 2024-12-24 09:48:01 -0000 (Tue, 24 Dec 2024) |
| EndedAt: 2024-12-24 09:52:29 -0000 (Tue, 24 Dec 2024) |
| EllapsedTime: 267.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: phenoTest.Rcheck |
| Warnings: 6 |
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:phenoTest.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings phenoTest_1.55.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/phenoTest.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘phenoTest/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘phenoTest’ version ‘1.55.0’
* checking package namespace information ... OK
* checking package dependencies ... INFO
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 ... WARNING
Found the following significant warnings:
Warning: program compiled against libxml 212 using older 211
See ‘/home/biocbuild/bbs-3.21-bioc/meat/phenoTest.Rcheck/00install.out’ for details.
* 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: program compiled against libxml 212 using older 211
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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Warning: program compiled against libxml 212 using older 211
'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 ... WARNING
Warning: program compiled against libxml 212 using older 211
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Warning: program compiled against libxml 212 using older 211
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Warning: program compiled against libxml 212 using older 211
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
Warning: program compiled against libxml 212 using older 211
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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
epheno-class.Rd: ExpressionSet-class, eSet-class,
VersionedBiobase-class, Versioned-class
gseaData-class.Rd: AssayData-class
gseaSignatures-class.Rd: AssayData-class
gseaSignaturesSign-class.Rd: AssayData-class
gseaSignaturesVar-class.Rd: AssayData-class
gseaSignificanceSign-class.Rd: AssayData-class
gseaSignificanceVar-class.Rd: AssayData-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... WARNING
Warning: program compiled against libxml 212 using older 211
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
* checking Rd \usage sections ... NOTE
Warning: program compiled against libxml 212 using older 211
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 ... WARNING
Warning: program compiled against libxml 212 using older 211
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ExpressionPhenoTest 8.202 0.176 8.404
* 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: 6 WARNINGs, 8 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/phenoTest.Rcheck/00check.log’
for details.
phenoTest.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL phenoTest ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘phenoTest’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning: program compiled against libxml 212 using older 211 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: program compiled against libxml 212 using older 211 ** testing if installed package can be loaded from final location Warning: program compiled against libxml 212 using older 211 ** testing if installed package keeps a record of temporary installation path * DONE (phenoTest)
phenoTest.Rcheck/phenoTest-Ex.timings
| name | user | system | elapsed | |
| ClusterPhenoTest | 0.173 | 0.004 | 0.178 | |
| ExpressionPhenoTest | 8.202 | 0.176 | 8.404 | |
| epheno-class | 0.002 | 0.000 | 0.001 | |
| epheno | 0.019 | 0.000 | 0.018 | |
| epheno2html | 0 | 0 | 0 | |
| eset | 0.135 | 0.000 | 0.135 | |
| eset.genelevel | 0.09 | 0.00 | 0.09 | |
| eset2genelevel | 0 | 0 | 0 | |
| findCopyNumber | 4.551 | 0.061 | 4.684 | |
| genesInArea | 0.306 | 0.012 | 0.320 | |
| getEsPositions | 0.257 | 0.000 | 0.257 | |
| getVars2test | 0.019 | 0.000 | 0.020 | |
| gsea | 0.256 | 0.000 | 0.256 | |
| gsea2html | 0.610 | 0.008 | 0.619 | |
| gseaData-class | 0.001 | 0.000 | 0.001 | |
| gseaSignatures-class | 0.001 | 0.000 | 0.001 | |
| gseaSignatures | 0.019 | 0.000 | 0.019 | |
| gseaSignaturesSign-class | 0.001 | 0.000 | 0.001 | |
| gseaSignaturesVar-class | 0 | 0 | 0 | |
| gseaSignificance | 0 | 0 | 0 | |
| gseaSignificanceSign-class | 0.001 | 0.000 | 0.000 | |
| gseaSignificanceVar-class | 0.000 | 0.000 | 0.001 | |
| heatmapPhenoTest | 0.368 | 0.000 | 0.370 | |
| pAdjust | 0.145 | 0.000 | 0.145 | |
| pca | 1.447 | 0.068 | 1.519 | |
| plot.gsea | 0 | 0 | 0 | |
| plot.gseaSignatures | 0.001 | 0.000 | 0.000 | |
| plots4epheno | 0.373 | 0.004 | 0.378 | |
| smoothCoxph | 0.175 | 0.000 | 0.176 | |
| summary.gsea | 0 | 0 | 0 | |
| summary.gseaSignificance | 0 | 0 | 0 | |
| write.html | 0 | 0 | 0 | |