Package: GenomicFeatures

Version: 1.3.15

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GenomicFeatures_1.3.15.tar.gz

StartedAt: 2011-03-17 16:25:30 -0700 (Thu, 17 Mar 2011)

EndedAt: 2011-03-17 16:31:42 -0700 (Thu, 17 Mar 2011)

EllapsedTime: 372.3 seconds

RetCode: 0

Status:  OK

CheckDir: GenomicFeatures.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/GenomicFeatures.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 'GenomicFeatures/DESCRIPTION' ... OK
* this is package 'GenomicFeatures' version '1.3.15'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GenomicFeatures' 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 ... NOTE
'library' or 'require' call not declared from: BSgenome.Celegans.UCSC.ce2
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'GenomicFeatures_unit_tests.R'
 OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'GenomicFeatures' ...
** R
** inst
** preparing package for lazy loading

Attaching package: 'IRanges'

The following object(s) are masked from 'package:base':

    Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (GenomicFeatures)

name	user	system	elapsed
DEFAULT_CIRC_SEQS	0.000	0.000	0.001
TranscriptDb-class	0.862	0.138	4.340
extractTranscriptsFromGenome	82.219	8.695	95.469
features	0.128	0.004	0.132
id2name	0.138	0.003	0.141
makeFeatureDbFromUCSC	5.558	0.139	28.397
makeTranscriptDb	0.148	0.009	0.156
makeTranscriptDbFromBiomart	1.425	0.051	20.329
makeTranscriptDbFromUCSC	7.188	0.152	20.754
saveFeatures	0.064	0.002	0.065
transcripts	0.404	0.002	0.406
transcriptsBy	1.706	0.042	1.750
transcriptsByOverlaps	0.257	0.001	0.259