virtualArray 1.2.1
Andreas Heider
| Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/virtualArray | | Last Changed Rev: 73898 / Revision: 74773 | | Last Changed Date: 2013-03-04 12:34:36 -0800 (Mon, 04 Mar 2013) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/virtualArray.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘virtualArray/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘virtualArray’ version ‘1.2.1’
* 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 whether package ‘virtualArray’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* 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 for unstated 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
nordi1p_getoutliers: no visible global function definition for
‘jarque.bera.test’
nordi1p_getoutliers: no visible global function definition for
‘grubbs.test’
nordi1p_getoutliers: no visible global function definition for
‘rm.outlier’
virtualArrayBuildfData: no visible global function definition for
‘biocLite’
virtualArrayCompile: no visible binding for global variable ‘mclapply’
virtualArrayExpressionSets: no visible binding for global variable
‘mclapply’
virtualArrayExpressionSets: no visible global function definition for
‘normalize.ExpressionSet’
virtualArrayLoadRaw: no visible binding for global variable ‘mclapply’
virtualArrayLoadRaw: no visible binding for global variable
‘rawdata_U133Plus2’
virtualArrayLoadRaw: no visible binding for global variable
‘rawdata_U219’
virtualArrayLoadRaw: no visible binding for global variable
‘rawdata_U133A’
virtualArrayComBat,data.frame: no visible global function definition
for ‘as.data.matrix’
* checking Rd files ... NOTE
prepare_Rd: normalize.ExpressionSet.gq.Rd:41-43: Dropping empty section \note
prepare_Rd: normalize.ExpressionSet.mc.Rd:40-42: Dropping empty section \note
prepare_Rd: normalize.ExpressionSet.mrs.Rd:40-42: Dropping empty section \note
prepare_Rd: normalize.ExpressionSet.nordi.Rd:39-41: Dropping empty section \note
prepare_Rd: normalize.ExpressionSet.qd.Rd:39-41: Dropping empty section \note
* 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 installed files from ‘inst/doc’ ... NOTE
The following files should probably not be installed:
‘virtualArray-016.pdf’, ‘virtualArray-022.pdf’,
‘virtualArray-023.pdf’
Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
virtualArrayBuildfData 7.74 0.472 24.356
virtualArrayBuildExprs 6.94 0.180 7.236
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK
NOTE: There were 3 notes.
See
‘/loc/home/biocbuild/bbs-2.11-bioc/meat/virtualArray.Rcheck/00check.log’
for details.
* installing *source* package ‘virtualArray’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘boxplot’ from package ‘graphics’ in package ‘affyPLM’
Creating a generic function for ‘hist’ from package ‘graphics’ in package ‘affyPLM’
Warning: replacing previous import ‘new’ when loading ‘methods’
Creating a generic function from function ‘virtualArrayComBat’ in package ‘virtualArray’
** help
*** installing help indices
** building package indices
** installing vignettes
‘virtualArray.Rnw’
** testing if installed package can be loaded
Creating a generic function for ‘boxplot’ from package ‘graphics’ in package ‘affyPLM’
Creating a generic function for ‘hist’ from package ‘graphics’ in package ‘affyPLM’
Warning: replacing previous import ‘new’ when loading ‘methods’
* DONE (virtualArray)