BioC 3.2: CHECK report for SNPchip on perceval

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: 2015-11-10 09:40:25 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 09:43:20 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 175.0 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 3.2.2 Patched (2015-10-08 r69496)
* 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 ‘2.16.0’
* 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 ... [14s/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 ... [23s/23s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
xyplot       8.416  0.212   8.769
xyplotLrrBaf 6.568  0.115   6.686
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.R’ [15s/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	0.117	0.003	0.119
getCytoband	0.037	0.007	0.058
plotIdiogram	0.533	0.036	0.588
xypanel	0.001	0.000	0.001
xyplot	8.416	0.212	8.769
xyplotLrrBaf	6.568	0.115	6.686