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: 2013-03-25 02:41:40 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:52:21 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 641.7 seconds

RetCode: 0

Status:  OK

CheckDir: GenomicFeatures.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/GenomicFeatures.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-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 ... [24s/24s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [192s/300s] OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
extractTranscriptsFromGenome 127.645 18.533 147.925
makeFeatureDbFromUCSC          8.627  0.357  67.980
makeTranscriptDbFromUCSC       5.483  0.157  27.990
makeTranscriptDbFromBiomart    2.508  0.159  22.059
TranscriptDb-class             1.014  0.343   6.835
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'GenomicFeatures_unit_tests.R' [104s/126s]
 [105s/127s] 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	0.005	0.005	0.010
FeatureDb-class	0.046	0.011	0.057
TranscriptDb-class	1.014	0.343	6.835
as-format-methods	2.515	0.026	2.543
extractTranscriptsFromGenome	127.645	18.533	147.925
features	0.102	0.011	0.113
getPromoterSeq-methods	4.036	0.618	4.717
id2name	0.089	0.021	0.111
makeFeatureDbFromUCSC	8.627	0.357	67.980
makeTranscriptDb	0.111	0.015	0.128
makeTranscriptDbFromBiomart	2.508	0.159	22.059
makeTranscriptDbFromGFF	2.089	0.082	2.180
makeTranscriptDbFromUCSC	5.483	0.157	27.990
makeTxDbPackage	0.729	0.053	0.805
saveFeatures	0.004	0.007	0.010
select-methods	0.374	0.038	0.413
transcripts	0.984	0.030	1.015
transcriptsBy	3.206	0.042	3.249
transcriptsByOverlaps	0.395	0.019	0.413