BioC 2.13: CHECK report for ArrayTools on perceval
This page was generated on 2014-04-05 09:52:10 -0700 (Sat, 05 Apr 2014).
ArrayTools 1.22.0 Arthur Li
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/ArrayTools | 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: ArrayTools |
Version: 1.22.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ArrayTools_1.22.0.tar.gz |
StartedAt: 2014-04-04 23:30:18 -0700 (Fri, 04 Apr 2014) |
EndedAt: 2014-04-04 23:32:19 -0700 (Fri, 04 Apr 2014) |
EllapsedTime: 121.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ArrayTools.Rcheck |
Warnings: 0 |
Command output
* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/ArrayTools.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 ‘ArrayTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ArrayTools’ version ‘1.22.0’
* 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 ‘ArrayTools’ can be installed ... [8s/8s] 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:
‘affy’ ‘Biobase’ ‘methods’
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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
preProcessGeneST: no visible binding for global variable
‘hugene10stCONTROL’
preProcessGeneST: no visible binding for global variable
‘mogene10stCONTROL’
regress: no visible global function definition for ‘permute.1’
* 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 ... OK
* 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’:
‘ArrayTools.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [19s/19s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
preProcess3prime 7.81 0.156 7.979
* 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 3 notes.
See
‘/Users/biocbuild/bbs-2.13-bioc/meat/ArrayTools.Rcheck/00check.log’
for details.
ArrayTools.Rcheck/00install.out:
* installing *source* package ‘ArrayTools’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘summary’ from package ‘base’ in package ‘ArrayTools’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ArrayTools)
ArrayTools.Rcheck/ArrayTools-Ex.timings:
name | user | system | elapsed
|
Output2HTML | 0.174 | 0.009 | 0.183 |
|
QC | 0.007 | 0.001 | 0.007 |
|
Sort | 0.213 | 0.006 | 0.219 |
|
contrastMatrix-class | 0.069 | 0.003 | 0.072 |
|
createExpressionSet | 0.101 | 0.001 | 0.102 |
|
createGSEAFiles | 0.008 | 0.000 | 0.009 |
|
createIndex | 0.346 | 0.005 | 0.351 |
|
createIngenuityFile | 0.092 | 0.001 | 0.093 |
|
designMatrix-class | 0.029 | 0.001 | 0.031 |
|
eSetExample | 0.008 | 0.001 | 0.009 |
|
exprsExample | 0.009 | 0.001 | 0.010 |
|
geneFilter | 4.269 | 0.086 | 4.355 |
|
interactionResult-class | 0.871 | 0.024 | 0.895 |
|
pDataExample | 0.011 | 0.001 | 0.013 |
|
postInteraction | 0.301 | 0.005 | 0.307 |
|
preProcess3prime | 7.810 | 0.156 | 7.979 |
|
preProcessGeneST | 0.043 | 0.012 | 0.055 |
|
qa3prime | 0.030 | 0.004 | 0.035 |
|
qaGeneST | 0.039 | 0.006 | 0.045 |
|
regress | 0.161 | 0.008 | 0.169 |
|
regressResult-class | 0.142 | 0.014 | 0.156 |
|
selectSigGene | 0.152 | 0.011 | 0.165 |
|
selectSigGeneInt | 0.382 | 0.016 | 0.399 |
|