BioC 2.13: CHECK report for ArrayTools on zin1
This page was generated on 2014-04-05 09:47:40 -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: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings ArrayTools_1.22.0.tar.gz |
StartedAt: 2014-04-04 23:38:13 -0700 (Fri, 04 Apr 2014) |
EndedAt: 2014-04-04 23:39:19 -0700 (Fri, 04 Apr 2014) |
EllapsedTime: 66.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ArrayTools.Rcheck |
Warnings: 0 |
Command output
* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/ArrayTools.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (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 ... [4s/4s] 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 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 ... [12s/12s] OK
* 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
‘/home/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 | 0.116 | 0.008 | 0.122 |
|
QC | 0.004 | 0.000 | 0.004 |
|
Sort | 0.124 | 0.004 | 0.131 |
|
contrastMatrix-class | 0.040 | 0.004 | 0.047 |
|
createExpressionSet | 0.080 | 0.000 | 0.082 |
|
createGSEAFiles | 0.004 | 0.000 | 0.007 |
|
createIndex | 0.272 | 0.004 | 0.274 |
|
createIngenuityFile | 0.068 | 0.000 | 0.068 |
|
designMatrix-class | 0.016 | 0.004 | 0.021 |
|
eSetExample | 0.008 | 0.000 | 0.006 |
|
exprsExample | 0.000 | 0.004 | 0.005 |
|
geneFilter | 2.772 | 0.012 | 2.787 |
|
interactionResult-class | 0.332 | 0.000 | 0.334 |
|
pDataExample | 0.004 | 0.000 | 0.004 |
|
postInteraction | 0.212 | 0.004 | 0.216 |
|
preProcess3prime | 4.576 | 0.072 | 4.653 |
|
preProcessGeneST | 0.024 | 0.000 | 0.023 |
|
qa3prime | 0.000 | 0.000 | 0.001 |
|
qaGeneST | 0.02 | 0.00 | 0.02 |
|
regress | 0.092 | 0.000 | 0.095 |
|
regressResult-class | 0.108 | 0.000 | 0.111 |
|
selectSigGene | 0.104 | 0.000 | 0.104 |
|
selectSigGeneInt | 0.268 | 0.000 | 0.268 |
|