Package: QUALIFIER

Version: 1.3.7

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings QUALIFIER_1.3.7.tar.gz

StartedAt: 2013-03-25 03:58:23 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 04:02:12 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 228.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: QUALIFIER.Rcheck

Warnings: 1

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/QUALIFIER.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘QUALIFIER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘QUALIFIER’ version ‘1.3.7’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘QUALIFIER’ can be installed ... [21s/26s] OK
* checking installed package size ... OK
* 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 ... WARNING
Scalable Robust Estimators with High Breakdown Point (version 1.3-02)

KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Error: .onLoad failed in loadNamespace() for ‘QUALIFIER’, details:
  call: RColorBrewer::brewer.pal(7, "Set1")
  error: could not find function "rgb"
In addition: Warning message:
no function found corresponding to methods exports from ‘rrcov’ for: ‘show’ 
Execution halted

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* 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 ... NOTE
.queryStats: no visible binding for global variable ‘stats’
makeQaTask: no visible binding for global variable ‘curRow’
plot.qaTask: no visible binding for global variable ‘value’
qa.panel.densityplot: no visible global function definition for
  ‘gateBoundary’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [10s/10s] 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
  ‘/home/biocbuild/bbs-2.12-bioc/meat/QUALIFIER.Rcheck/00check.log’
for details.

* installing *source* package ‘QUALIFIER’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘QUALIFIER.Rnw’ 
** testing if installed package can be loaded
* DONE (QUALIFIER)

name	user	system	elapsed
getQAStats	0.028	0.004	0.032
plot-methods	0.032	0.000	0.033
qaCheck-methods	0.036	0.004	0.038
qaReport	0.020	0.000	0.018