Package: GenomicFeatures

Version: 1.5.5

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GenomicFeatures_1.5.5.tar.gz

StartedAt: 2011-05-09 14:50:01 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 14:58:08 -0700 (Mon, 09 May 2011)

EllapsedTime: 487.6 seconds

RetCode: 0

Status:  OK

CheckDir: GenomicFeatures.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/GenomicFeatures.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-24 r55634)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicFeatures/DESCRIPTION’ ... OK
* this is package ‘GenomicFeatures’ version ‘1.5.5’
* 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 ... NOTE
.getMetaDataValue: no visible global function definition for ‘error’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘GenomicFeatures_unit_tests.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 ‘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 ...
*** tangling vignette sources ...
   ‘GenomicFeatures.Rnw’ 
   ‘examples.Rnw’ 
** testing if installed package can be loaded

* DONE (GenomicFeatures)

name	user	system	elapsed
DEFAULT_CIRC_SEQS	0.000	0.000	0.001
TranscriptDb-class	1.130	0.147	1.449
extractTranscriptsFromGenome	101.148	17.396	128.733
features	0.187	0.008	0.266
id2name	0.200	0.007	0.242
makeFeatureDbFromUCSC	7.488	0.235	31.633
makeTranscriptDb	0.212	0.015	0.241
makeTranscriptDbFromBiomart	1.795	0.095	20.678
makeTranscriptDbFromUCSC	3.770	0.119	24.777
makeTxDbPackage	0.006	0.001	0.006
saveFeatures	0.097	0.003	0.101
transcripts	0.565	0.006	0.586
transcriptsBy	1.967	0.015	1.986
transcriptsByOverlaps	0.350	0.004	0.355