Package: GenomicFeatures

Version: 1.11.16

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GenomicFeatures_1.11.16.tar.gz

StartedAt: 2013-03-24 05:38:22 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 05:50:21 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 718.7 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 beta (2013-03-21 r62346)
* 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 '1.11.16'
* 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 ... [29s/30s] 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 ... [197s/304s] OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
extractTranscriptsFromGenome 126.056 21.062 151.050
makeFeatureDbFromUCSC         10.026  0.477  70.401
makeTranscriptDbFromUCSC       5.649  0.178  27.300
getPromoterSeq-methods         3.616  0.658   5.106
makeTranscriptDbFromBiomart    2.555  0.215  22.651
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'GenomicFeatures_unit_tests.R' [113s/134s]
 [113s/135s] 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
   'GenomicFeatures.Rnw' 
** testing if installed package can be loaded
* DONE (GenomicFeatures)

name	user	system	elapsed
DEFAULT_CIRC_SEQS	0.007	0.003	0.011
FeatureDb-class	0.071	0.010	0.081
TranscriptDb-class	0.982	0.138	1.127
as-format-methods	2.517	0.034	2.626
extractTranscriptsFromGenome	126.056	21.062	151.050
features	0.103	0.010	0.117
getPromoterSeq-methods	3.616	0.658	5.106
id2name	0.104	0.019	0.124
makeFeatureDbFromUCSC	10.026	0.477	70.401
makeTranscriptDb	0.139	0.018	0.159
makeTranscriptDbFromBiomart	2.555	0.215	22.651
makeTranscriptDbFromGFF	2.783	0.110	2.897
makeTranscriptDbFromUCSC	5.649	0.178	27.300
makeTxDbPackage	0.710	0.050	0.775
saveFeatures	0.004	0.007	0.011
select-methods	0.322	0.034	0.360
transcripts	0.810	0.018	0.829
transcriptsBy	2.540	0.028	2.573
transcriptsByOverlaps	0.348	0.012	0.360