virtualArray 1.4.1
Andreas Heider
| Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/virtualArray | | Last Changed Rev: 76869 / Revision: 81334 | | Last Changed Date: 2013-05-24 10:07:32 -0700 (Fri, 24 May 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | [ WARNINGS ] | OK |
* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/virtualArray.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'virtualArray/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'virtualArray' version '1.4.1'
* package encoding: latin1
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
'multicore' 'BiocParallel'
* 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 'virtualArray' can be installed ... [23s/23s] OK
* checking installed package size ... OK
* checking package directory ... 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
File 'virtualArray/R/onLoad.R':
.onLoad calls:
message("To support our work please cite:")
print(citation("virtualArray"))
message("Thanks.")
Package startup functions should use 'packageStartupMessage' to
generate messages.
See section 'Good practice' in '?.onAttach'.
nordi1p_getoutliers: no visible global function definition for
'rm.outlier'
virtualArrayBuildfData: no visible global function definition for
'biocinstallRepos'
virtualArrayExpressionSets: no visible global function definition for
'biocinstallRepos'
virtualArrayExpressionSets: no visible global function definition for
'register'
virtualArrayExpressionSets: no visible global function definition for
'MulticoreParam'
virtualArrayExpressionSets: no visible binding for global variable
'bplapply'
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:42-44: 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 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' ... NOTE
The following files should probably not be installed:
'virtualArray-016.pdf'
Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... WARNING
checking a package with encoding 'latin1' in an ASCII locale
[30s/34s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
virtualArrayBuildfData 7.851 0.367 11.951
virtualArrayBuildExprs 6.672 0.128 6.806
* 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
WARNING: There was 1 warning.
NOTE: There were 4 notes.
See
'/Users/biocbuild/bbs-2.12-bioc/meat/virtualArray.Rcheck/00check.log'
for details.
* installing *source* package 'virtualArray' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for 'hist' from package 'graphics' in package 'affyPLM'
Warning: replacing previous import 'new' when loading 'methods'
Warning: replacing previous import 'density' when loading 'stats'
Warning: replacing previous import 'installed.packages' when loading 'utils'
Warning: replacing previous import 'read.csv' when loading 'utils'
Warning: replacing previous import 'read.table' when loading 'utils'
Warning: replacing previous import 'write.table' when loading 'utils'
Creating a generic function from function 'virtualArrayComBat' in package 'virtualArray'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'hist' from package 'graphics' in package 'affyPLM'
Warning: replacing previous import 'new' when loading 'methods'
Warning: replacing previous import 'density' when loading 'stats'
Warning: replacing previous import 'installed.packages' when loading 'utils'
Warning: replacing previous import 'read.csv' when loading 'utils'
Warning: replacing previous import 'read.table' when loading 'utils'
Warning: replacing previous import 'write.table' when loading 'utils'
To support our work please cite:
To cite package 'virtualArray' in publications use:
Andreas Heider and R<fc>diger Alt (2013). virtualArray: a
R/bioconductor package to merge raw data from different microarray
platforms. R package version 1.4.1.
A BibTeX entry for LaTeX users is
@Article{,
title = {virtualArray: a R/bioconductor package to merge raw data from different microarray platforms},
author = {{Andreas Heider} and {R<fc>diger Alt}},
year = {2013},
note = {R package version 1.4.1},
journal = {BMC Bioinformatics},
volume = {14},
pages = {75},
}
Thanks.
* DONE (virtualArray)