BioC 2.14: CHECK report for SNPchip on zin2

Package: SNPchip

Version: 2.10.0

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings SNPchip_2.10.0.tar.gz

StartedAt: 2014-10-08 02:53:29 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 02:55:58 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 149.9 seconds

RetCode: 0

Status:  OK

CheckDir: SNPchip.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings SNPchip_2.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/SNPchip.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘2.10.0’
* 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 ... [11s/11s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [23s/23s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
xyplotLrrBaf 8.661  0.096   8.788
xyplot       7.128  0.092   7.380
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘doRUnit.R’ [13s/13s]
 [13s/13s] 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
  ‘/home/biocbuild/bbs-2.14-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	0.476	0.004	0.481
getCytoband	0.036	0.000	0.033
plotIdiogram	0.568	0.044	0.613
xypanel	0.000	0.000	0.001
xyplot	7.128	0.092	7.380
xyplotLrrBaf	8.661	0.096	8.788