Package: ArrayExpress

Version: 1.17.1

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ArrayExpress_1.17.1.tar.gz

StartedAt: 2012-06-20 21:49:03 -0700 (Wed, 20 Jun 2012)

EndedAt: 2012-06-20 21:55:38 -0700 (Wed, 20 Jun 2012)

EllapsedTime: 395.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: ArrayExpress.Rcheck

Warnings: 3

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/ArrayExpress.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'ArrayExpress/DESCRIPTION' ... OK
* this is package 'ArrayExpress' version '1.17.1'
* 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 whether package 'ArrayExpress' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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
magetab2bioc: no visible global function definition for 'nonAB'
magetab2bioc: no visible global function definition for 'AB'
magetab2bioc : <anonymous>: no visible global function definition for
  'AB'
magetab2bioc : <anonymous>: no visible global function definition for
  'nonAB'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'ae2bioc'
All user-level objects in a package should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'getAE':
getAE
  Code: function(input, path = getwd(), type = "raw", extract = TRUE)
  Docs: function(input, path = getwd(), type = "full", extract = TRUE)
  Mismatches in argument default values:
    Name: 'type' Code: "raw" Docs: "full"

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'ArrayExpress'
  'dataCols'
Documented arguments not in \usage in documentation object 'ArrayExpress':
  'rawcol'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... 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

WARNING: There were 3 warnings.
NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/ArrayExpress.Rcheck/00check.log'
for details.

* installing *source* package 'ArrayExpress' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'ArrayExpress.Rnw' 
** testing if installed package can be loaded

* DONE (ArrayExpress)

name	user	system	elapsed
ArrayExpress	13.214	3.660	104.191
getAE	5.801	1.308	40.589
magetab2bioc	0.000	0.000	0.001
procset	0	0	0
queryAE	167.142	0.412	173.404