Package: GeneTraffic

Version: 1.25.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings GeneTraffic_1.25.0.tar.gz

StartedAt: 2011-05-09 12:35:27 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 12:36:33 -0700 (Mon, 09 May 2011)

EllapsedTime: 66.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: GeneTraffic.Rcheck

Warnings: 2

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/GeneTraffic.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneTraffic/DESCRIPTION’ ... OK
* this is package ‘GeneTraffic’ version ‘1.25.0’
* checking package name space 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 examples ... WARNING
Found the following significant warnings:

  Warning: ‘zip.file.extract’ is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* checking PDF version of manual ... OK

WARNING: There were 2 warnings, see
  ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/GeneTraffic.Rcheck/00check.log’
for details

* installing *source* package ‘GeneTraffic’ ...
** R
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

** 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	0.000	0.000	0.001
GTLoadExpression	0.004	0.000	0.003
GTLogin	0	0	0
GTLogout	0	0	0
GTServer-class	0.004	0.000	0.001
GTServer	0.000	0.000	0.001