BioC 2.14: CHECK report for GenomicFiles on petty

Package: GenomicFiles

Version: 1.0.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GenomicFiles_1.0.1.tar.gz

StartedAt: 2014-10-07 22:11:43 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:21:25 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 581.9 seconds

RetCode: 0

Status:  OK

CheckDir: GenomicFiles.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GenomicFiles_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/GenomicFiles.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicFiles/DESCRIPTION’ ... OK
* this is package ‘GenomicFiles’ version ‘1.0.1’
* 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 ‘GenomicFiles’ can be installed ... [35s/36s] 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 ... OK
* 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 ... [234s/206s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
reduceBy-methods      117.876 31.384 150.061
BamFileViews-class     40.368  7.531  19.353
BigWigFileViews-class  17.357  0.146  17.581
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘GenomicFiles_unit_tests.R’ [17s/17s]
 [18s/18s] 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

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

name	user	system	elapsed
BamFileViews-class	40.368	7.531	19.353
BigWigFileViews-class	17.357	0.146	17.581
FaFileViews-class	0.484	0.010	0.510
GenomicFileViews-class	0.052	0.002	0.055
reduceBy-methods	117.876	31.384	150.061
registry-utils	0.003	0.000	0.003