BioC 3.0: CHECK report for GGBase on perceval

Package: GGBase

Version: 3.28.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GGBase_3.28.0.tar.gz

StartedAt: 2015-04-10 02:10:40 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 02:17:42 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 422.4 seconds

RetCode: 0

Status:  OK

CheckDir: GGBase.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 --no-multiarch GGBase_3.28.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/GGBase.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GGBase/DESCRIPTION’ ... OK
* this is package ‘GGBase’ version ‘3.28.0’
* 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 ‘GGBase’ can be installed ... [32s/34s] 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
'library' or 'require' call to ‘snpStats’ which was already attached by Depends.
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
regressOut: no visible global function definition for ‘assay<-’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [34s/40s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
MAFfilter 7.676  0.450  12.585
plot_EvG  5.054  0.337   5.559
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘MAFfilter.R’ [24s/24s]
  Running ‘make.R’ [22s/23s]
  Running ‘plot_EvG.R’ [25s/25s]
 [72s/73s] 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/GGBase.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
MAFfilter	7.676	0.450	12.585
clipPCs	0.001	0.000	0.001
externalize	0.001	0.000	0.000
make_smlSet	4.336	0.125	4.482
plot_EvG	5.054	0.337	5.559
rsid-class	0.003	0.001	0.003
smlSet-class	0.003	0.001	0.003