Package: genomeIntervals

Version: 1.12.0

Command: /home/biocbuild/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings genomeIntervals_1.12.0.tar.gz

StartedAt: 2012-09-24 01:06:18 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 01:07:31 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 73.7 seconds

RetCode: 0

Status:  OK

CheckDir: genomeIntervals.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/genomeIntervals.Rcheck’
* using R version 2.15.1 (2012-06-22)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genomeIntervals/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genomeIntervals’ version ‘1.12.0’
* 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 whether package ‘genomeIntervals’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘benchmarking-tests.R’
  Comparing ‘benchmarking-tests.Rout’ to ‘benchmarking-tests.Rout.save’ ...13,29d12
< 
< Attaching package: 'BiocGenerics'
< 
< The following object(s) are masked from 'package:stats':
< 
<     xtabs
< 
< The following object(s) are masked from 'package:base':
< 
<     Filter, Find, Map, Position, Reduce, anyDuplicated, cbind,
<     colnames, duplicated, eval, get, intersect, lapply, mapply, mget,
<     order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int,
<     rownames, sapply, setdiff, table, tapply, union, unique
< 
< Warning messages:
< 1: replacing previous import 'coerce' when loading 'intervals' 
< 2: replacing previous import 'initialize' when loading 'intervals' 
  Running ‘consistency-tests.R’
  Running ‘fullShow.R’
 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

* installing *source* package ‘genomeIntervals’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘coerce’ when loading ‘intervals’
Warning: replacing previous import ‘initialize’ when loading ‘intervals’
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘genomeIntervals.Rnw’ 
** testing if installed package can be loaded
Warning: replacing previous import ‘coerce’ when loading ‘intervals’
Warning: replacing previous import ‘initialize’ when loading ‘intervals’

* DONE (genomeIntervals)

name	user	system	elapsed
GenomeIntervals-constructor	0.080	0.004	0.084
Genome_intervals-class	0.052	0.004	0.054
Genome_intervals_stranded-class	0.076	0.000	0.076
c.Genome_intervals	0.100	0.004	0.104
core_annotated	0.06	0.00	0.06
distance_to_nearest-methods	0.304	0.000	0.308
getGffAttribute	0.356	0.040	0.393
interval_overlap-methods	0.160	0.004	0.159
interval_set_operations-methods	1.200	0.000	1.205
parseGffAttributes	0.032	0.004	0.033
readGFF3	0.048	0.000	0.049