Package: GenomicFeatures

Version: 1.12.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GenomicFeatures_1.12.1.tar.gz

StartedAt: 2013-05-01 05:57:51 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 06:11:17 -0700 (Wed, 01 May 2013)

EllapsedTime: 806.6 seconds

RetCode: 0

Status:  OK

CheckDir: GenomicFeatures.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/GenomicFeatures.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GenomicFeatures/DESCRIPTION' ... OK
* this is package 'GenomicFeatures' version '1.12.1'
* 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 'GenomicFeatures' can be installed ... [28s/29s] 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 ... NOTE
.setseqnameStyle: no visible binding for global variable 'txdb'
* 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 installed files from 'inst/doc' ... OK
* checking examples ... [199s/295s] OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
extractTranscriptsFromGenome 125.986 21.686 153.922
makeFeatureDbFromUCSC         10.030  0.500  57.607
makeTranscriptDbFromUCSC       5.683  0.182  25.379
getPromoterSeq-methods         3.932  0.771   6.177
makeTranscriptDbFromBiomart    2.498  0.184  21.328
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'GenomicFeatures_unit_tests.R' [133s/228s]
 [134s/228s] 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

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/GenomicFeatures.Rcheck/00check.log'
for details.

* installing *source* package 'GenomicFeatures' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GenomicFeatures)

name	user	system	elapsed
DEFAULT_CIRC_SEQS	0.009	0.005	0.014
FeatureDb-class	0.057	0.008	0.065
TranscriptDb-class	1.057	0.256	4.041
as-format-methods	2.845	0.047	2.953
extractTranscriptsFromGenome	125.986	21.686	153.922
features	0.107	0.009	0.140
getPromoterSeq-methods	3.932	0.771	6.177
id2name	0.087	0.015	0.134
makeFeatureDbFromUCSC	10.030	0.500	57.607
makeTranscriptDb	0.160	0.025	0.185
makeTranscriptDbFromBiomart	2.498	0.184	21.328
makeTranscriptDbFromGFF	2.841	0.129	3.057
makeTranscriptDbFromUCSC	5.683	0.182	25.379
makeTxDbPackage	0.610	0.036	0.698
saveFeatures	0.003	0.005	0.010
select-methods	0.336	0.034	0.379
transcripts	0.925	0.037	0.985
transcriptsBy	2.616	0.030	2.679
transcriptsByOverlaps	0.339	0.011	0.354