phenoTest 1.16.0
Evarist Planet
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/phenoTest | | Last Changed Rev: 102591 / Revision: 109384 | | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings phenoTest_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/phenoTest.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘phenoTest/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘phenoTest’ version ‘1.16.0’
* 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 ... [40s/41s] 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:
‘annotate’ ‘BMA’ ‘ggplot2’ ‘Heatplus’ ‘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’
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<-’
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’
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 : .local: no visible global function definition
for ‘featureNames’
[,epheno-ANY-ANY-ANY : .local: no visible global function definition
for ‘exprs<-’
[,epheno-ANY-ANY-ANY : .local: no visible global function definition
for ‘exprs’
[,epheno-ANY-ANY-ANY : .local: no visible global function definition
for ‘pData’
[,epheno-ANY-ANY-ANY : .local: 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’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
S3 methods shown with full name in documentation object 'plot.gseaData':
‘plot.gseaData’
S3 methods shown with full name in documentation object 'plot.gseaSignatures':
‘plot.gseaSignaturesSign’
S3 methods shown with full name in documentation object 'summary.gseaData':
‘summary.gseaData’
S3 methods shown with full name in documentation object 'summary.gseaSignificance':
‘summary.gseaSignificanceSign’
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [43s/43s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
ExpressionPhenoTest 11.413 0.124 11.549
findCopyNumber 6.798 0.299 7.208
* 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
‘/Users/biocbuild/bbs-3.1-bioc/meat/phenoTest.Rcheck/00check.log’
for details.
* installing *source* package ‘phenoTest’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Warning: replacing previous import by ‘GSEABase::union’ when loading ‘HTSanalyzeR’
Warning in namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]], c(lib.loc, :
No generic function found corresponding to requested imported methods for "head" from package "AnnotationDbi" (malformed exports?)
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Warning: replacing previous import by ‘GSEABase::union’ when loading ‘HTSanalyzeR’
Warning in namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]], c(lib.loc, :
No generic function found corresponding to requested imported methods for "head" from package "AnnotationDbi" (malformed exports?)
* DONE (phenoTest)