BioC 3.1: CHECK report for GGBase on petty

Package: GGBase

Version: 3.30.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GGBase_3.30.1.tar.gz

StartedAt: 2015-10-08 23:20:01 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 23:24:49 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 288.0 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 GGBase_3.30.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/GGBase.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘3.30.1’
* 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 ... [24s/24s] 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 ... 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 ... [27s/31s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
MAFfilter 5.956  0.402  10.199
plot_EvG  5.690  0.335   6.097
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘MAFfilter.R’ [16s/16s]
  Running ‘make.R’ [16s/16s]
  Running ‘plot_EvG.R’ [17s/17s]
 [50s/50s] 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/GGBase.Rcheck/00check.log’
for details.

* installing *source* package ‘GGBase’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (GGBase)

name	user	system	elapsed
MAFfilter	5.956	0.402	10.199
clipPCs	0.001	0.000	0.001
externalize	0.001	0.000	0.001
make_smlSet	4.045	0.143	4.191
plot_EvG	5.690	0.335	6.097
rsid-class	0.003	0.000	0.002
smlSet-class	0.002	0.000	0.002