BioC 2.13: CHECK report for SNPchip on perceval

Package: SNPchip

Version: 2.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SNPchip_2.8.0.tar.gz

StartedAt: 2014-04-05 04:27:50 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 04:32:28 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 278.3 seconds

RetCode: 0

Status:  OK

CheckDir: SNPchip.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/SNPchip.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SNPchip/DESCRIPTION’ ... OK
* this is package ‘SNPchip’ version ‘2.8.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SNPchip’ can be installed ... [21s/21s] 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
‘:::’ call which should be ‘::’: ‘lattice:::xyplot’
  See the note in ?`:::` about the use of this operator.
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 ... NOTE
dataFrameSummarizedExperiment: no visible binding for global variable
  ‘j’
* checking Rd files ... NOTE
prepare_Rd: arrangeFigs.Rd:35-36: Dropping empty section \examples
prepare_Rd: dataFrame.Rd:43-44: Dropping empty section \examples
prepare_Rd: latticeFigs.Rd:27-29: Dropping empty section \details
prepare_Rd: latticeFigs.Rd:37-38: Dropping empty section \seealso
prepare_Rd: latticeFigs.Rd:39-40: Dropping empty section \examples
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [44s/45s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
xyplotLrrBaf 17.569  0.393  18.289
xyplot       13.705  0.301  14.424
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘doRUnit.R’ [24s/25s]
 [25s/25s] 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 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/SNPchip.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
centromere	0.800	0.033	0.850
getCytoband	0.057	0.006	0.107
plotIdiogram	0.908	0.092	1.034
xypanel	0.019	0.003	0.021
xyplot	13.705	0.301	14.424
xyplotLrrBaf	17.569	0.393	18.289