BioC 2.12: CHECK report for genomeIntervals on petty

Package: genomeIntervals

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genomeIntervals_1.16.0.tar.gz

StartedAt: 2013-10-08 22:32:27 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:34:17 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 109.7 seconds

RetCode: 0

Status:  OK

CheckDir: genomeIntervals.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/genomeIntervals.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 'genomeIntervals/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'genomeIntervals' version '1.16.0'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'genomeIntervals' can be installed ... [7s/7s] 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 ... 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [8s/8s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'benchmarking-tests.R' [8s/8s]
  Comparing 'benchmarking-tests.Rout' to 'benchmarking-tests.Rout.save' ...13,36d12
< 
< Attaching package: 'BiocGenerics'
< 
< The following objects are masked from 'package:parallel':
< 
<     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
<     clusterExport, clusterMap, parApply, parCapply, parLapply,
<     parLapplyLB, parRapply, parSapply, parSapplyLB
< 
< The following object is masked from 'package:stats':
< 
<     xtabs
< 
< The following objects are masked from 'package:base':
< 
<     Filter, Find, Map, Position, Reduce, anyDuplicated, as.data.frame,
<     cbind, colnames, duplicated, eval, get, intersect, lapply, mapply,
<     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
<     rbind, rep.int, rownames, sapply, setdiff, sort, table, tapply,
<     union, unique, unlist
< 
< Warning messages:
< 1: replacing previous import 'coerce' when loading 'intervals' 
< 2: replacing previous import 'initialize' when loading 'intervals' 
  Running 'consistency-tests.R' [8s/9s]
  Running 'fullShow.R' [1s/1s]
 [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 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
** 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	0.212	0.001	0.217
Genome_intervals-class	0.136	0.004	0.144
Genome_intervals-ordering	0.174	0.003	0.177
Genome_intervals_stranded-class	0.119	0.002	0.130
c.Genome_intervals	0.160	0.006	0.179
core_annotated	0.100	0.004	0.120
distance_to_nearest-methods	0.442	0.004	0.448
getGffAttribute	0.898	0.105	1.077
interval_overlap-methods	0.267	0.004	0.275
interval_set_operations-methods	1.922	0.013	1.987
parseGffAttributes	0.091	0.003	0.095
readGFF3	0.206	0.003	0.212