Package: genomeIntervals

Version: 1.9.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings genomeIntervals_1.9.0.tar.gz

StartedAt: 2011-05-09 12:35:54 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 12:37:08 -0700 (Mon, 09 May 2011)

EllapsedTime: 73.8 seconds

RetCode: 0

Status:  OK

CheckDir: genomeIntervals.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/genomeIntervals.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* 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 ‘1.9.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘benchmarking-tests.R’
  Comparing ‘benchmarking-tests.Rout’ to ‘benchmarking-tests.Rout.save’ ... OK
  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
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘genomeIntervals.Rnw’ 
** testing if installed package can be loaded

* DONE (genomeIntervals)

name	user	system	elapsed
GenomeIntervals-constructor	0.184	0.004	0.195
Genome_intervals-class	0.084	0.000	0.085
Genome_intervals_stranded-class	0.092	0.000	0.093
c.Genome_intervals	0.112	0.000	0.115
core_annotated	0.068	0.004	0.072
distance_to_nearest-methods	0.332	0.000	0.334
getGffAttribute	0.356	0.044	0.398
interval_overlap-methods	0.216	0.000	0.216
interval_set_operations-methods	1.672	0.000	1.669
parseGffAttributes	0.06	0.00	0.06
readGFF3	0.072	0.004	0.078