lumi 2.11.6
Pan Du
| Snapshot Date: 2013-03-23 17:02:20 -0700 (Sat, 23 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/lumi | | Last Changed Rev: 73539 / Revision: 74756 | | Last Changed Date: 2013-02-14 10:44:34 -0800 (Thu, 14 Feb 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | WARNINGS | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | WARNINGS | OK |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
| pelham | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | [ WARNINGS ] | OK |
* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/lumi.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'lumi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'lumi' version '2.11.6'
* 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 'lumi' can be installed ... [47s/48s] OK
* checking installed package size ... NOTE
installed size is 12.0Mb
sub-directories of 1Mb or more:
data 3.6Mb
doc 7.7Mb
* 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
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
* checking Rd files ... NOTE
prepare_Rd: getChrInfo.Rd:23-25: Dropping empty section \details
prepare_Rd: getChrInfo.Rd:29-31: Dropping empty section \references
prepare_Rd: getChrInfo.Rd:38-40: Dropping empty section \seealso
prepare_Rd: getChrInfo.Rd:41-44: Dropping empty section \examples
prepare_Rd: importMethyIDAT.Rd:44-47: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'pairs-methods':
\S4method{pairs}{ExpressionSet}
Code: function(x, ..., smoothScatter = FALSE, logMode = TRUE, subset
= 5000, fold = 2, dotColor = 1, highlight = NULL,
highlightColor = 2, main = NULL, checkTransform =
TRUE)
Docs: function(x, ..., smoothScatter = FALSE, logMode = TRUE, subset
= 5000, fold = 2, dotColor = 1, highlight = NULL,
highlightColor = 2, main = NULL)
Argument names in code not in docs:
checkTransform
* 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 examples ... [450s/460s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
lumiMethyStatus 181.158 11.935 196.024
nuID2RefSeqID 35.995 0.211 36.355
getNuIDMappingInfo 31.871 0.278 33.357
nuID2EntrezID 23.452 0.171 24.034
plotGammaFit 12.152 0.815 13.010
methylationCall 11.312 0.673 12.196
getChipInfo 10.246 0.627 11.111
gammaFitEM 9.848 0.548 10.452
MAplot-methods 8.752 0.140 9.704
probeID2nuID 8.454 0.346 8.835
nuID2targetID 8.270 0.355 8.671
nuID2IlluminaID 7.578 0.368 7.963
nuID2probeID 7.450 0.349 7.822
targetID2nuID 7.355 0.328 7.711
LumiBatch-class 4.913 0.135 5.538
* 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 3 notes.
See
'/Users/biocbuild/bbs-2.12-bioc/meat/lumi.Rcheck/00check.log'
for details.
* installing *source* package 'lumi' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'image' when loading 'graphics'
Warning: replacing previous import 'nleqslv' when loading 'nleqslv'
** help
*** installing help indices
** building package indices
** installing vignettes
'IlluminaAnnotation.Rnw'
'lumi.Rnw'
'lumi_VST_evaluation.Rnw'
'methylationAnalysis.Rnw'
** testing if installed package can be loaded
Warning: replacing previous import 'image' when loading 'graphics'
Warning: replacing previous import 'nleqslv' when loading 'nleqslv'
Warning: ignoring .First.lib() for package 'lumi'
* DONE (lumi)