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BioC 2.12: CHECK report for RPA on george2

This page was generated on 2013-10-09 09:37:34 -0700 (Wed, 09 Oct 2013).

Package 565/671HostnameOS / ArchBUILDCHECKBUILD BIN
RPA 1.16.0
Leo Lahti
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/RPA
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: RPA
Version: 1.16.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings RPA_1.16.0.tar.gz
StartedAt: 2013-10-09 04:42:46 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 04:43:55 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 69.1 seconds
RetCode: 0
Status:  OK 
CheckDir: RPA.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/RPA.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 ‘RPA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RPA’ version ‘1.16.0’
* 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 ‘RPA’ can be installed ... [6s/6s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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
File ‘RPA/R/firstlib.R’:
  .onLoad calls:
    packageStartupMessage("\nRPA Copyright (C) 2008-2013 Leo Lahti.\nThis program comes with ABSOLUTELY NO WARRANTY.\nThis is free software, and you are welcome to redistribute it under the FreeBSD open source license.\n")

See section ‘Good practice’ in '?.onAttach'.
* 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 ... [3s/3s] 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/RPA.Rcheck/00check.log’
for details.

RPA.Rcheck/00install.out:

* installing *source* package ‘RPA’ ...
** R
** inst
** preparing package for lazy loading
     Package    LibPath                                   Item      
[1,] "affydata" "/home/biocbuild/bbs-2.12-bioc/R/library" "Dilution"
     Title                        
[1,] "AffyBatch instance Dilution"
in method for ‘show’ with signature ‘"rpa"’: no definition for class “rpa”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
     Package    LibPath                                   Item      
[1,] "affydata" "/home/biocbuild/bbs-2.12-bioc/R/library" "Dilution"
     Title                        
[1,] "AffyBatch instance Dilution"
* DONE (RPA)

RPA.Rcheck/RPA-Ex.timings:

nameusersystemelapsed
RPA-package0.0080.0000.008
RPA.iteration0.0040.0000.004
RPA.preprocess0.0040.0000.007
collect.hyperparameters0.0120.0000.013
d.update.fast0.0120.0000.009
estimate.affinities0.0080.0000.008
estimate.hyperparameters0.0080.0000.009
frpa0.0040.0000.007
get.batches0.0040.0000.006
get.probe.matrix0.0080.0000.006
get.probe.parameters0.0040.0000.006
hyperparameter.update0.0160.0000.016
online.quantile0.0080.0000.010
probe.parameters.tolist0.0080.0000.006
probe.performance0.0080.0000.006
probetable0.0040.0000.006
rpa0.0080.0000.009
rpa.complete0.0040.0000.005
rpa.fit0.0040.0000.005
rpa.online0.1680.0000.170
rpa.plot0.0080.0000.007
rpa.summarize0.0080.0000.006
rpaplot0.0080.0000.009
sample.probeset0.0040.0000.006
summarize.batch0.0080.0000.007
summarize.batches0.0080.0000.006
updating.hyperparameters0.0040.0000.006