BioC 3.0: CHECK report for plethy on perceval

Package: plethy

Version: 1.4.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch plethy_1.4.3.tar.gz

StartedAt: 2015-04-10 04:53:57 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 04:59:33 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 336.6 seconds

RetCode: 0

Status:  OK

CheckDir: plethy.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 plethy_1.4.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/plethy.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 ‘plethy/DESCRIPTION’ ... OK
* this is package ‘plethy’ version ‘1.4.3’
* 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 ‘plethy’ can be installed ... [14s/17s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘csv.to.table’ ‘find.break.ranges.integer’ ‘fix.time’ ‘multi.grep’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ... [33s/36s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
utilities 9.743  1.720  12.588
parsing   5.017  1.304   6.922
plethy    4.792  1.381   7.205
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [143s/151s]
 [143s/151s] 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 was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/plethy.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
BuxcoDB	1.254	0.104	1.522
add_query_funcs	0.423	0.036	0.523
dbImport	0.701	0.038	0.904
parsing	5.017	1.304	6.922
plethy	4.792	1.381	7.205
utilities	9.743	1.720	12.588