BioC 2.13: CHECK report for RPA on zin1

Package: RPA

Version: 1.18.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings RPA_1.18.0.tar.gz

StartedAt: 2014-04-05 03:42:30 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:43:01 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 31.6 seconds

RetCode: 0

Status:  OK

CheckDir: RPA.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/RPA.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.18.0’
* 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 ... [3s/3s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘affy’ ‘affydata’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Missing or unexported object: ‘affy::normalize’
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 ... 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘RPA.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [1s/1s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/RPA.Rcheck/00check.log’
for details.

* installing *source* package ‘RPA’ ...
** R
** inst
** preparing package for lazy loading
     Package    LibPath                                   Item      
[1,] "affydata" "/home/biocbuild/bbs-2.13-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-2.13-bioc/R/library" "Dilution"
     Title                        
[1,] "AffyBatch instance Dilution"
* DONE (RPA)

name	user	system	elapsed
RPA-package	0.000	0.000	0.002
RPA.iteration	0.004	0.000	0.002
RPA.preprocess	0.000	0.000	0.003
collect.hyperparameters	0.004	0.000	0.002
d.update.fast	0.000	0.000	0.002
estimate.affinities	0.004	0.000	0.002
estimate.hyperparameters	0.004	0.000	0.002
frpa	0.000	0.000	0.002
get.batches	0.004	0.000	0.002
get.probe.matrix	0.004	0.000	0.002
get.probe.parameters	0.004	0.000	0.002
hyperparameter.update	0.004	0.004	0.007
online.quantile	0.000	0.000	0.003
probe.parameters.tolist	0.004	0.000	0.002
probe.performance	0.048	0.004	0.049
probetable	0.000	0.000	0.003
rpa	0.004	0.000	0.003
rpa.complete	0.000	0.000	0.002
rpa.fit	0.000	0.004	0.002
rpa.online	0.000	0.000	0.002
rpa.plot	0.000	0.000	0.002
rpa.summarize	0.004	0.000	0.002
rpaplot	0.000	0.000	0.002
sample.probeset	0.000	0.004	0.003
summarize.batch	0.000	0.004	0.003
summarize.batches	0.000	0.000	0.003
updating.hyperparameters	0.004	0.000	0.003