Package: GenomicFeatures

Version: 1.11.16

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings GenomicFeatures_1.11.16.tar.gz

StartedAt: 2013-03-25 01:54:35 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:07:50 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 795.2 seconds

RetCode: 0

Status:  OK

CheckDir: GenomicFeatures.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/GenomicFeatures.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* 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 ‘1.11.16’
* 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 ... [34s/34s] 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 ... [186s/302s] OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
extractTranscriptsFromGenome 108.755 22.901 136.564
makeFeatureDbFromUCSC         10.916  0.404  78.722
makeTranscriptDbFromUCSC       5.768  0.072  29.356
makeTranscriptDbFromBiomart    2.980  0.048  21.633
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘GenomicFeatures_unit_tests.R’ [126s/145s]
 [127s/145s] 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
  ‘/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	0.012	0.000	0.010
FeatureDb-class	0.068	0.004	0.071
TranscriptDb-class	0.961	0.096	1.109
as-format-methods	2.900	0.020	2.921
extractTranscriptsFromGenome	108.755	22.901	136.564
features	0.136	0.008	0.144
getPromoterSeq-methods	3.484	0.420	3.970
id2name	0.112	0.008	0.119
makeFeatureDbFromUCSC	10.916	0.404	78.722
makeTranscriptDb	0.133	0.000	0.132
makeTranscriptDbFromBiomart	2.980	0.048	21.633
makeTranscriptDbFromGFF	3.104	0.008	3.362
makeTranscriptDbFromUCSC	5.768	0.072	29.356
makeTxDbPackage	0.704	0.016	0.734
saveFeatures	0.016	0.000	0.014
select-methods	0.572	0.004	0.576
transcripts	1.024	0.016	1.040
transcriptsBy	3.125	0.016	3.152
transcriptsByOverlaps	0.448	0.000	0.447