BioC 2.12: CHECK report for ensemblVEP on petty

Package: ensemblVEP

Version: 1.0.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ensemblVEP_1.0.5.tar.gz

StartedAt: 2013-10-08 22:15:59 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:23:45 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 466.1 seconds

RetCode: 0

Status:  OK

CheckDir: ensemblVEP.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/ensemblVEP.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'ensemblVEP/DESCRIPTION' ... OK
* this is package 'ensemblVEP' version '1.0.5'
* 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 'ensemblVEP' can be installed ... [36s/37s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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
File 'ensemblVEP/R/zzz.R':
  .onLoad calls:
    packageStartupMessage(msg)

See section 'Good practice' in '?.onAttach'.
* 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 examples ... [26s/73s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
ensemblVEP        4.535  0.432  35.909
parseCSQToGRanges 2.213  0.208  17.592
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'runTests.R' [22s/45s]
 [22s/46s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/ensemblVEP.Rcheck/00check.log'
for details.

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

name	user	system	elapsed
VEPParam-class	0.493	0.013	0.508
ensemblVEP	4.535	0.432	35.909
parseCSQToGRanges	2.213	0.208	17.592