Package: GenomicFeatures

Version: 1.11.6

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings GenomicFeatures_1.11.6.tar.gz

StartedAt: 2013-01-16 02:53:10 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 03:01:34 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 503.9 seconds

RetCode: 0

Status:  OK

CheckDir: GenomicFeatures.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/GenomicFeatures.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicFeatures/DESCRIPTION’ ... OK
* this is package ‘GenomicFeatures’ version ‘1.11.6’
* 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
extractTranscriptsFromGenome 81.950 13.256  96.290
makeFeatureDbFromUCSC         5.260  0.128  23.694
makeTranscriptDbFromUCSC      2.657  0.036  10.596
makeTranscriptDbFromBiomart   2.264  0.036  20.652
* 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

NOTE: There was 1 note.
See
  ‘/loc/home/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	0.412	0.004	0.414
FeatureDb-class	0.052	0.004	0.056
TranscriptDb-class	0.732	0.052	0.790
as-format-methods	2.608	0.008	2.617
extractTranscriptsFromGenome	81.950	13.256	96.290
features	0.100	0.000	0.103
getPromoterSeq-methods	2.316	0.264	2.950
id2name	0.076	0.004	0.081
makeFeatureDbFromUCSC	5.260	0.128	23.694
makeTranscriptDb	0.080	0.000	0.083
makeTranscriptDbFromBiomart	2.264	0.036	20.652
makeTranscriptDbFromGFF	2.192	0.016	2.221
makeTranscriptDbFromUCSC	2.657	0.036	10.596
makeTxDbPackage	0.448	0.008	0.472
saveFeatures	0.004	0.000	0.004
select-methods	0.320	0.004	0.322
transcripts	0.612	0.004	0.613
transcriptsBy	2.044	0.008	2.056
transcriptsByOverlaps	0.328	0.004	0.334