BioC 2.12: CHECK report for SNPchip on george2

Package: SNPchip

Version: 2.6.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings SNPchip_2.6.0.tar.gz

StartedAt: 2013-10-09 05:03:07 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 05:08:51 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 343.4 seconds

RetCode: 0

Status:  OK

CheckDir: SNPchip.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/SNPchip.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SNPchip/DESCRIPTION’ ... OK
* this is package ‘SNPchip’ version ‘2.6.0’
* 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 ... [24s/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 ... 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 ... 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [43s/52s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
xyplotLrrBaf 22.597  0.304  27.628
xyplot        7.501  0.092   8.244
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘doRUnit.R’ [20s/25s]
 [20s/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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.12-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	0.728	0.024	0.826
getCytoband	0.492	0.012	0.721
plotIdiogram	0.740	0.080	1.053
xypanel	0.016	0.000	0.019
xyplot	7.501	0.092	8.244
xyplotLrrBaf	22.597	0.304	27.628