virtualArray 1.8.0
Andreas Heider
| Snapshot Date: 2014-04-22 17:03:48 -0700 (Tue, 22 Apr 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/virtualArray | | Last Changed Rev: 88838 / Revision: 89373 | | Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | WARNINGS | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | WARNINGS | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | [ WARNINGS ] | OK |
| morelia | Mac OS X Mavericks (10.9.2) / x86_64 | OK | WARNINGS | OK |
* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/virtualArray.Rcheck’
* using R version 3.1.0 (2014-04-10)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.8.0’
* package encoding: latin1
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘multicore’
* 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 ... [24s/24s] WARNING
Found the following significant warnings:
Warning: replacing previous import by ‘utils::relist’ when loading ‘virtualArray’
Warning: replacing previous import by ‘methods::new’ when loading ‘virtualArray’
Warning: replacing previous import by ‘stats::density’ when loading ‘virtualArray’
Warning: replacing previous import by ‘utils::installed.packages’ when loading ‘virtualArray’
Warning: replacing previous import by ‘utils::read.csv’ when loading ‘virtualArray’
Warning: replacing previous import by ‘utils::read.table’ when loading ‘virtualArray’
Warning: replacing previous import by ‘utils::write.table’ when loading ‘virtualArray’
See ‘/Users/biocbuild/bbs-2.14-bioc/meat/virtualArray.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘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 ... NOTE
Packages in Depends field not imported from:
‘plyr’ ‘preprocessCore’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
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
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’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [38s/41s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
virtualArrayBuildfData 10.753 0.481 15.017
virtualArrayBuildExprs 8.739 0.163 8.919
virtualArrayBuildSampleInfo 4.991 0.081 5.095
* 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
WARNING: There was 1 warning.
NOTE: There were 5 notes.
See
‘/Users/biocbuild/bbs-2.14-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
Warning: replacing previous import by ‘utils::relist’ when loading ‘virtualArray’
Creating a generic function for ‘hist’ from package ‘graphics’ in package ‘affyPLM’
Warning: replacing previous import by ‘methods::new’ when loading ‘virtualArray’
Warning: replacing previous import by ‘stats::density’ when loading ‘virtualArray’
Warning: replacing previous import by ‘utils::installed.packages’ when loading ‘virtualArray’
Warning: replacing previous import by ‘utils::read.csv’ when loading ‘virtualArray’
Warning: replacing previous import by ‘utils::read.table’ when loading ‘virtualArray’
Warning: replacing previous import by ‘utils::write.table’ when loading ‘virtualArray’
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
Warning: replacing previous import by ‘utils::relist’ when loading ‘virtualArray’
Creating a generic function for ‘hist’ from package ‘graphics’ in package ‘affyPLM’
Warning: replacing previous import by ‘methods::new’ when loading ‘virtualArray’
Warning: replacing previous import by ‘stats::density’ when loading ‘virtualArray’
Warning: replacing previous import by ‘utils::installed.packages’ when loading ‘virtualArray’
Warning: replacing previous import by ‘utils::read.csv’ when loading ‘virtualArray’
Warning: replacing previous import by ‘utils::read.table’ when loading ‘virtualArray’
Warning: replacing previous import by ‘utils::write.table’ when loading ‘virtualArray’
To support our work please cite:
To cite package 'virtualArray' in publications use:
Andreas Heider and Rüdiger Alt (2013). virtualArray: a R/bioconductor
package to merge raw data from different microarray platforms. R
package version 1.8.0.
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 {Rüdiger Alt}},
year = {2013},
note = {R package version 1.8.0},
journal = {BMC Bioinformatics},
volume = {14},
pages = {75},
}
Thanks.
* DONE (virtualArray)