BioC 2.14: CHECK report for RGalaxy on petty

Package: RGalaxy

Version: 1.8.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RGalaxy_1.8.1.tar.gz

StartedAt: 2014-10-07 23:49:16 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:51:29 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 133.1 seconds

RetCode: 0

Status:  OK

CheckDir: RGalaxy.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RGalaxy_1.8.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/RGalaxy.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RGalaxy/DESCRIPTION’ ... OK
* this is package ‘RGalaxy’ version ‘1.8.1’
* 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 ... [8s/8s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘digest’ ‘methods’ ‘optparse’ ‘XML’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': ‘tools:::md5sum’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘tools:::.Rd_get_argument_table’ ‘tools:::.Rd_get_metadata’
  ‘tools:::fetchRdDB’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘parseSectionFromText’
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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... [11s/11s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
probeLookup 6.574  0.165   7.051
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [19s/20s]
 [20s/20s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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
** testing if installed package can be loaded
* DONE (RGalaxy)

name	user	system	elapsed
GalaxyClasses	0.051	0.003	0.054
GalaxyConfig-class	0.005	0.001	0.006
GalaxyInputFile-class	0.008	0.000	0.007
GalaxyOutput-class	0.016	0.000	0.016
RserveConnection-class	0.004	0.000	0.004
addTwoNumbers	0.002	0.000	0.004
addTwoNumbersWithTest	0.067	0.004	0.071
anotherTestFunction	0.023	0.004	0.028
functionToGalaxify	0.091	0.014	0.112
galaxy	0.007	0.002	0.009
getFriendlyName	0.001	0.000	0.002
probeLookup	6.574	0.165	7.051
utilities	0.003	0.000	0.003