phenoTest 1.19.0
Evarist Planet
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/phenoTest | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings phenoTest_1.19.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/phenoTest.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (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 ‘1.19.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘phenoTest’ can be installed ... [22s/22s] 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 ... OK
* 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 ‘pData’
ClusterPhenoTest : <anonymous>: no visible global function definition
for ‘pData’
ExpressionPhenoTest : mycoxph: no visible global function definition
for ‘pData’
ExpressionPhenoTest : mycoxph: no visible global function definition
for ‘bic.surv’
ExpressionPhenoTest: no visible global function definition for ‘exprs’
ExpressionPhenoTest: no visible global function definition for ‘pData’
ExpressionPhenoTest : <anonymous>: no visible global function
definition for ‘pData’
ExpressionPhenoTest: no visible binding for global variable ‘y’
ExpressionPhenoTest: no visible global function definition for
‘featureNames’
ExpressionPhenoTest: no visible global function definition for
‘annotation’
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
‘pData’
epheno2html : export2html: no visible global function definition for
‘exprs’
epheno2html : export2html : myFun: no visible global function
definition for ‘featureNames’
epheno2html : export2html : myFun: no visible global function
definition for ‘pData’
epheno2html : export2html : myFun: no visible global function
definition for ‘exprs’
eset2genelevel: no visible global function definition for ‘annotation’
eset2genelevel: no visible global function definition for
‘featureNames<-’
eset2genelevel: no visible global function definition for
‘annotation<-’
getEsPositions: no visible global function definition for ‘annotation’
getEsPositions: no visible global function definition for
‘featureNames’
gsea.go: no visible global function definition for ‘featureNames’
gsea.kegg: no visible global function definition for ‘featureNames’
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’
pca: no visible global function definition for ‘exprs’
pca.2d: no visible global function definition for ‘pData’
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’
[,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
‘pData<-’
barplotSignatures,epheno-list : <anonymous>: no visible global function
definition for ‘featureNames’
barplotSignatures,epheno-list : <anonymous> : <anonymous>: no visible
global function definition for ‘featureNames’
barplotSignifSignatures,epheno-list : <anonymous>: no visible global
function definition for ‘featureNames’
barplotSignifSignatures,epheno-list : myFun1 : <anonymous>: no visible
global function definition for ‘featureNames’
boxplotSignatures,epheno-list : <anonymous>: no visible global function
definition for ‘featureNames’
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’
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’
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 ‘heatmap_plus’
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 ‘exprs’
pAdjust,epheno: no visible global function definition for ‘exprs<-’
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’
Undefined global functions or variables:
Term annotation annotation<- bic.surv coord_cartesian exprs exprs<-
fData featureNames featureNames<- geom_point ggtitle heatmap_plus
pData pData<- pc1 pc2 qplot theme y
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [27s/27s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
ExpressionPhenoTest 5.951 0.024 5.976
findCopyNumber 5.515 0.016 5.531
* 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: 4 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/phenoTest.Rcheck/00check.log’
for details.