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BioC 2.12: CHECK report for minfi on george2

This page was generated on 2013-10-09 09:37:48 -0700 (Wed, 09 Oct 2013).

Package 415/671HostnameOS / ArchBUILDCHECKBUILD BIN
minfi 1.6.0
Kasper Daniel Hansen
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/minfi
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 

Summary

Package: minfi
Version: 1.6.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings minfi_1.6.0.tar.gz
StartedAt: 2013-10-09 03:17:52 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 03:35:13 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 1041.0 seconds
RetCode: 0
Status:  OK 
CheckDir: minfi.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/minfi.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘minfi/DESCRIPTION’ ... OK
* this is package ‘minfi’ version ‘1.6.0’
* 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 ‘minfi’ can be installed ... [30s/30s] 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 ... OK
* checking Rd files ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [421s/482s] OK
Examples with CPU or elapsed time > 5s
                                     user system elapsed
preprocessSwan                    144.057  0.336 167.513
plotBetasByType                    79.065  0.196  79.826
densityBeanPlot                    34.203  0.484  34.940
read.450k.exp                      24.690  0.104  46.665
detectionP                         21.513  0.124  21.715
read.450k                          21.377  0.236  35.668
preprocessIllumina                 20.742  0.096  20.834
densityPlot                        19.189  0.260  19.454
preprocessRaw                      14.049  0.176  14.224
IlluminaMethylationManifest-class  10.205  0.460  10.786
controlStripPlot                    7.792  0.248   8.197
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [211s/296s]
 [211s/297s] OK
* 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

minfi.Rcheck/00install.out:

* installing *source* package ‘minfi’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (minfi)

minfi.Rcheck/minfi-Ex.timings:

nameusersystemelapsed
GenomicMethylSet-class0.5480.0040.549
GenomicRatioSet-class0.0120.0040.019
IlluminaMethylationManifest-class10.205 0.46010.786
MethylSet-class0.0000.0080.010
RGChannelSet-class0.0040.0080.009
controlStripPlot7.7920.2488.197
densityBeanPlot34.203 0.48434.940
densityPlot19.189 0.26019.454
detectionP21.513 0.12421.715
dmpFinder2.5560.2522.969
logit20.0040.0000.007
mdsPlot2.9320.1923.126
plotBetasByType79.065 0.19679.826
plotCpg0.5080.0080.518
preprocessIllumina20.742 0.09620.834
preprocessRaw14.049 0.17614.224
preprocessSwan144.057 0.336167.513
qcReport0.1480.0040.312
read.450k21.377 0.23635.668
read.450k.exp24.690 0.10446.665
read.450k.sheet0.1600.0120.351