lumi 2.12.0
Pan Du
| 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/lumi | | Last Changed Rev: 75263 / Revision: 81334 | | Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 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 | OK | OK |
* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/lumi.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'lumi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'lumi' version '2.12.0'
* 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 whether package 'lumi' can be installed ... OK
* checking installed package size ... NOTE
installed size is 12.1Mb
sub-directories of 1Mb or more:
data 3.6Mb
doc 7.8Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... 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 installed files from 'inst/doc' ... OK
* checking examples ...
** running examples for arch 'i386' ... [307s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
lumiMethyStatus 139.99 0.00 140.01
nuID2EntrezID 10.92 0.01 10.93
getNuIDMappingInfo 9.76 0.05 10.02
plotGammaFit 9.47 0.00 9.47
nuID2RefSeqID 9.35 0.00 9.35
MAplot-methods 8.14 0.04 8.19
getChipInfo 7.47 0.58 14.47
methylationCall 7.92 0.00 7.92
targetID2nuID 7.35 0.01 7.37
gammaFitEM 7.07 0.03 7.12
nuID2IlluminaID 6.90 0.03 6.92
nuID2probeID 6.33 0.00 6.35
nuID2targetID 6.19 0.00 6.19
probeID2nuID 6.02 0.03 6.05
** running examples for arch 'x64' ... [338s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
lumiMethyStatus 140.93 0.00 140.97
getNuIDMappingInfo 20.80 0.01 20.81
nuID2EntrezID 16.26 0.00 16.25
nuID2RefSeqID 15.11 0.00 15.12
getChipInfo 10.19 0.37 10.56
plotGammaFit 9.07 0.01 9.08
gammaFitEM 8.90 0.02 8.93
methylationCall 8.72 0.00 8.72
MAplot-methods 8.22 0.04 8.27
nuID2IlluminaID 8.20 0.00 8.21
probeID2nuID 7.94 0.00 7.94
nuID2targetID 7.85 0.03 7.88
nuID2probeID 7.64 0.03 7.67
targetID2nuID 6.69 0.02 6.71
* 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
'E:/biocbld/bbs-2.12-bioc/meat/lumi.Rcheck/00check.log'
for details.
install for i386
* 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
** 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'
install for x64
* installing *source* package 'lumi' ...
** 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'
* MD5 sums
packaged installation of 'lumi' as lumi_2.12.0.zip
* DONE (lumi)