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BioC 2.12: CHECK report for ARRmNormalization on george2

This page was generated on 2013-10-09 09:38:00 -0700 (Wed, 09 Oct 2013).

Package 51/671HostnameOS / ArchBUILDCHECKBUILD BIN
ARRmNormalization 1.0.0
Jean-Philippe Fortin
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/ARRmNormalization
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: ARRmNormalization
Version: 1.0.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings ARRmNormalization_1.0.0.tar.gz
StartedAt: 2013-10-09 00:15:16 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 00:21:36 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 380.0 seconds
RetCode: 0
Status:  OK 
CheckDir: ARRmNormalization.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/ARRmNormalization.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 ‘ARRmNormalization/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ARRmNormalization’ version ‘1.0.0’
* 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 ‘ARRmNormalization’ can be installed ... [7s/7s] 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 ... NOTE
getQuantiles: no visible binding for global variable ‘ProbesType’
normalizeARRm: no visible binding for global variable ‘ProbesType’
* 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 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 ... [334s/342s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
normalizeARRm   218.838 10.248 233.617
getCoefficients  35.322  2.764  39.147
getQuantiles     22.325  0.968  24.459
quantilePlots    19.321  0.468  19.800
positionPlots    18.293  0.936  19.268
* 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 was 1 note.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/ARRmNormalization.Rcheck/00check.log’
for details.

ARRmNormalization.Rcheck/00install.out:

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

ARRmNormalization.Rcheck/ARRmNormalization-Ex.timings:

nameusersystemelapsed
ProbesType3.2400.0683.750
getBackground0.0560.0000.053
getCoefficients35.322 2.76439.147
getDesignInfo0.0080.0040.011
getQuantiles22.325 0.96824.459
normalizeARRm218.838 10.248233.617
positionPlots18.293 0.93619.268
quantilePlots19.321 0.46819.800