BioC 3.2: CHECK report for SNPchip on oaxaca

Package: SNPchip

Version: 2.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SNPchip_2.16.0.tar.gz

StartedAt: 2016-04-23 04:34:17 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 04:37:13 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 175.5 seconds

RetCode: 0

Status:  OK

CheckDir: SNPchip.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 SNPchip_2.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/SNPchip.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SNPchip/DESCRIPTION’ ... OK
* this is package ‘SNPchip’ version ‘2.16.0’
* 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 ... [13s/14s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
coerce,BafLrrSetList-RangedSummarizedExperiment : .local: no visible
  global function definition for ‘DataFrame’
coerce,BafLrrSetList-RangedSummarizedExperiment : .local: no visible
  global function definition for ‘SimpleList’
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [21s/26s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
xyplot       7.713  0.184  11.626
xyplotLrrBaf 5.476  0.141   6.013
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.R’ [14s/15s]
 [15s/15s] 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
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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	0.129	0.002	0.131
getCytoband	0.038	0.004	0.069
plotIdiogram	0.653	0.028	0.714
xypanel	0.001	0.000	0.001
xyplot	7.713	0.184	11.626
xyplotLrrBaf	5.476	0.141	6.013