Package: genomeIntervals

Version: 1.7.4

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genomeIntervals_1.7.4.tar.gz

StartedAt: 2011-03-17 16:24:57 -0700 (Thu, 17 Mar 2011)

EndedAt: 2011-03-17 16:26:17 -0700 (Thu, 17 Mar 2011)

EllapsedTime: 79.3 seconds

RetCode: 0

Status:  OK

CheckDir: genomeIntervals.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/genomeIntervals.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'genomeIntervals/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'genomeIntervals' version '1.7.4'
* 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' ...12a13,19
> 
> Welcome to Bioconductor
> 
>   Vignettes contain introductory material. To view, type
>   'openVignette()'. To cite Bioconductor, see
>   'citation("Biobase")' and for packages 'citation(pkgname)'.
> 
  Running 'consistency-tests.R'
 OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'genomeIntervals' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for "sort" in "genomeIntervals"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (genomeIntervals)

name	user	system	elapsed
GenomeIntervals-constructor	0.137	0.002	0.139
Genome_intervals-class	0.084	0.001	0.084
Genome_intervals_stranded-class	0.091	0.002	0.092
c.Genome_intervals	0.095	0.002	0.097
core_annotated	0.051	0.001	0.051
distance_to_nearest-methods	0.324	0.001	0.325
getGffAttribute	0.392	0.047	0.438
interval_overlap-methods	0.192	0.001	0.193
interval_set_operations-methods	1.454	0.002	1.457
parseGffAttributes	0.046	0.000	0.047
readGFF3	0.062	0.001	0.063