BioC 2.13: CHECK report for phenoTest on perceval
This page was generated on 2014-04-05 09:52:33 -0700 (Sat, 05 Apr 2014).
phenoTest 1.10.0 Evarist Planet
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/phenoTest | Last Changed Rev: 81642 / Revision: 88450 | Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | |
moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | [ OK ] | OK |
Summary
Package: phenoTest |
Version: 1.10.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch phenoTest_1.10.0.tar.gz |
StartedAt: 2014-04-05 03:20:37 -0700 (Sat, 05 Apr 2014) |
EndedAt: 2014-04-05 03:31:29 -0700 (Sat, 05 Apr 2014) |
EllapsedTime: 652.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: phenoTest.Rcheck |
Warnings: 0 |
Command output
* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/phenoTest.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.10.0’
* 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 ... [58s/66s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
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’ calls to packages already attached by Depends:
‘ggplot2’ ‘gridExtra’
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’ ‘gridExtra’ ‘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’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ExpressionPhenoTest: no visible binding for global variable ‘y’
pca.2d: no visible binding for global variable ‘pc1’
pca.2d: no visible binding for global variable ‘pc2’
pca.multipleDim: no visible binding for global variable ‘dummy1’
pca.multipleDim: no visible binding for global variable ‘dummy2’
pca.multipleDim: no visible binding for global variable ‘colour’
* 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 the 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
‘phenoTest.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [55s/56s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
ExpressionPhenoTest 9.653 0.397 10.176
findCopyNumber 8.488 0.603 9.394
* 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
NOTE: There were 5 notes.
See
‘/Users/biocbuild/bbs-2.13-bioc/meat/phenoTest.Rcheck/00check.log’
for details.
phenoTest.Rcheck/00install.out:
* installing *source* package ‘phenoTest’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘graphics::image’ when loading ‘hopach’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘graphics::image’ when loading ‘hopach’
* DONE (phenoTest)
phenoTest.Rcheck/phenoTest-Ex.timings:
name | user | system | elapsed
|
ClusterPhenoTest | 0.262 | 0.019 | 0.286 |
|
ExpressionPhenoTest | 9.653 | 0.397 | 10.176 |
|
epheno-class | 0.017 | 0.007 | 0.024 |
|
epheno | 0.039 | 0.008 | 0.048 |
|
epheno2html | 0.005 | 0.006 | 0.011 |
|
eset | 0.137 | 0.014 | 0.161 |
|
eset.genelevel | 0.093 | 0.009 | 0.115 |
|
eset2genelevel | 0.002 | 0.003 | 0.006 |
|
findCopyNumber | 8.488 | 0.603 | 9.394 |
|
genesInArea | 0.362 | 0.019 | 0.463 |
|
getEsPositions | 0.378 | 0.017 | 0.407 |
|
getGo | 0.013 | 0.004 | 0.020 |
|
getKegg | 0.002 | 0.002 | 0.005 |
|
getVars2test | 0.040 | 0.005 | 0.048 |
|
gsea | 0.417 | 0.034 | 0.463 |
|
gsea.kegg.go | 0.036 | 0.009 | 0.046 |
|
gsea2html | 1.904 | 0.063 | 2.029 |
|
gseaData-class | 0.016 | 0.004 | 0.021 |
|
gseaSignatures-class | 0.004 | 0.002 | 0.007 |
|
gseaSignatures | 0.045 | 0.012 | 0.056 |
|
gseaSignaturesSign-class | 0.005 | 0.003 | 0.008 |
|
gseaSignaturesVar-class | 0.005 | 0.005 | 0.009 |
|
gseaSignificance | 0.002 | 0.004 | 0.006 |
|
gseaSignificanceSign-class | 0.004 | 0.004 | 0.008 |
|
gseaSignificanceVar-class | 0.003 | 0.004 | 0.008 |
|
heatmapPhenoTest | 0.384 | 0.022 | 0.512 |
|
pAdjust | 0.046 | 0.007 | 0.053 |
|
pca | 2.289 | 0.084 | 2.456 |
|
plot.gsea | 0.015 | 0.004 | 0.018 |
|
plot.gseaSignatures | 0.002 | 0.003 | 0.006 |
|
plots4epheno | 0.090 | 0.012 | 0.130 |
|
smoothCoxph | 0.186 | 0.014 | 0.226 |
|
summary.gsea | 0.017 | 0.003 | 0.020 |
|
summary.gseaSignificance | 0.022 | 0.005 | 0.029 |
|
write.html | 0.021 | 0.006 | 0.026 |
|