BioC 2.12: CHECK report for GEOquery on petty

Package: GEOquery

Version: 2.26.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GEOquery_2.26.2.tar.gz

StartedAt: 2013-10-08 22:33:56 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:35:20 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 83.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: GEOquery.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/GEOquery.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GEOquery/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GEOquery' version '2.26.2'
* 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 'GEOquery' can be installed ... [7s/7s] OK
* checking installed package size ... NOTE
  installed size is 13.3Mb
  sub-directories of 1Mb or more:
    extdata  12.8Mb
* 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 ... WARNING
'library' or 'require' call not declared from: 'RUnit'
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 'GEOquery/R/zzz.R':
  .onLoad calls:
    packageStartupMessage("Setting options('download.file.method.GEOquery'='curl')")
    packageStartupMessage("Setting options('download.file.method.GEOquery'='auto')")

See section 'Good practice' in '?.onAttach'.

runTests: no visible global function definition for 'defineTestSuite'
runTests: no visible global function definition for 'runTestSuite'
runTests: no visible global function definition for 'printTextProtocol'
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [4s/4s] 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 was 1 warning.
NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/GEOquery.Rcheck/00check.log'
for details.

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

name	user	system	elapsed
GDS2MA	0.007	0.001	0.007
getGEO	0.010	0.001	0.010
getGEOSuppFiles	0.008	0.000	0.008
getGEOfile	0.109	0.001	0.109
getGSEDataTables	0.054	0.006	0.973