lumi 2.16.0
Pan Du
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/lumi | | Last Changed Rev: 88838 / Revision: 95116 | | Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | WARNINGS | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ WARNINGS ] | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch lumi_2.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/lumi.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘lumi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘lumi’ version ‘2.16.0’
* 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 ‘lumi’ can be installed ... [65s/67s] OK
* checking installed package size ... NOTE
installed size is 9.5Mb
sub-directories of 1Mb or more:
data 3.6Mb
doc 5.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘Biobase’
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 ... WARNING
'::' or ':::' import not declared from: ‘bigmemoryExtras’
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 ... OK
* 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:39-42: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Packages unavailable to check Rd xrefs: ‘bigmemoryExtras’, ‘hdrcde’
* 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 ... [433s/454s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
lumiMethyStatus 147.817 10.884 165.846
nuID2RefSeqID 43.555 0.143 46.297
getNuIDMappingInfo 41.429 0.286 44.054
nuID2EntrezID 25.893 0.106 27.726
MAplot-methods 10.529 0.085 11.517
getChipInfo 9.204 0.621 10.737
methylationCall 8.633 0.514 9.559
plotGammaFit 8.288 0.839 9.156
nuID2targetID 8.311 0.211 8.552
targetID2nuID 7.794 0.195 8.017
nuID2IlluminaID 7.706 0.211 8.416
nuID2probeID 7.679 0.197 8.505
probeID2nuID 7.450 0.217 7.736
gammaFitEM 7.578 0.038 8.101
LumiBatch-class 4.813 0.071 5.085
* 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 4 notes.
See
‘/Users/biocbuild/bbs-2.14-bioc/meat/lumi.Rcheck/00check.log’
for details.
* installing *source* package ‘lumi’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘graphics::image’ when loading ‘methylumi’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘graphics::image’ when loading ‘methylumi’
* DONE (lumi)