Package: RGalaxy

Version: 1.3.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RGalaxy_1.3.6.tar.gz

StartedAt: 2013-03-20 04:12:09 -0700 (Wed, 20 Mar 2013)

EndedAt: 2013-03-20 04:13:46 -0700 (Wed, 20 Mar 2013)

EllapsedTime: 96.6 seconds

RetCode: 0

Status:  OK

CheckDir: RGalaxy.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/RGalaxy.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'RGalaxy/DESCRIPTION' ... OK
* this is package 'RGalaxy' version '1.3.6'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'RSclient'
* 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 'RGalaxy' can be installed ... [7s/7s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package 'knitr' is specified in field VignetteBuilder but is in neither
Imports nor Depends.
* 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 ... 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [8s/9s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'runTests.R' [14s/14s]
 [14s/15s] 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

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/RGalaxy.Rcheck/00check.log'
for details.

* installing *source* package 'RGalaxy' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'RGalaxy-vignette.Rmd' 
processing file: RGalaxy-vignette.Rmd
output file: /Users/biocbuild/bbs-2.12-bioc/meat/RGalaxy.Rcheck/RGalaxy/doc/RGalaxy-vignette.R
** testing if installed package can be loaded
* DONE (RGalaxy)

name	user	system	elapsed
GalaxyClasses	0.053	0.016	0.074
GalaxyConfig-class	0.017	0.008	0.024
GalaxyInputFile-class	0.018	0.009	0.026
GalaxyOutput-class	0.018	0.006	0.024
RserveConnection-class	0.011	0.006	0.016
addTwoNumbers	0.063	0.009	0.072
addTwoNumbersWithTest	0.074	0.020	0.105
anotherTestFunction	0.032	0.018	0.067
functionToGalaxify	0.072	0.022	0.103
galaxy	0.018	0.013	0.030
getFriendlyName	0.010	0.006	0.015
probeLookup	4.698	0.222	4.981
utilities	0.011	0.006	0.017