Package: GeneTraffic

Version: 1.25.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GeneTraffic_1.25.0.tar.gz

StartedAt: 2011-08-27 02:37:32 -0700 (Sat, 27 Aug 2011)

EndedAt: 2011-08-27 02:38:49 -0700 (Sat, 27 Aug 2011)

EllapsedTime: 77.5 seconds

RetCode: 1

Status:  ERROR

CheckDir: GeneTraffic.Rcheck

Warnings: NA

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/GeneTraffic.Rcheck'
* using R Under development (unstable) (2011-08-03 r56617)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GeneTraffic/DESCRIPTION' ... OK
* this is package 'GeneTraffic' version '1.25.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GeneTraffic' 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 ... OK
* 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 ... WARNING
Assignments in \usage in documentation object 'GTLogin':
  session <- GTLogin(server)

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 examples ... ERROR
Running examples in 'GeneTraffic-Ex.R' failed
The error most likely occurred in:

> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GTLoadExpression
> ### Title: Reads from a GeneTraffic project summary file
> ### Aliases: GTLoadExpression
> ### Keywords: IO
> 
> ### ** Examples
> 
>     #From a file:
> 	eset <- GTLoadExpression(filename="Project.zip")
Error: 'zip.file.extract' is defunct.
Use 'unzip' instead.
See help("Defunct")
Execution halted

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

* DONE (GeneTraffic)

name	user	system	elapsed
GTGetProjectList	0	0	0
GTGetProjectSummary	0.001	0.000	0.000