BioC 2.12: CHECK report for GenomicFeatures on petty

Package: GenomicFeatures

Version: 1.12.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GenomicFeatures_1.12.4.tar.gz

StartedAt: 2013-10-08 22:32:34 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:45:33 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 779.0 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 3.0.1 (2013-05-16)
* 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 '1.12.4'
* 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 ... [32s/33s] 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 ... [213s/315s] OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
extractTranscriptsFromGenome 134.205 19.720 155.608
makeFeatureDbFromUCSC         12.389  0.451  71.932
makeTranscriptDbFromUCSC       7.141  0.161  31.547
makeTranscriptDbFromBiomart    3.091  0.156  19.393
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'GenomicFeatures_unit_tests.R' [132s/147s]
 [132s/148s] 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	0.006	0.004	0.009
FeatureDb-class	0.079	0.008	0.087
TranscriptDb-class	1.288	0.158	1.582
as-format-methods	3.161	0.029	3.196
extractTranscriptsFromGenome	134.205	19.720	155.608
features	0.136	0.008	0.145
getPromoterSeq-methods	3.897	0.650	4.648
id2name	0.125	0.013	0.138
makeFeatureDbFromUCSC	12.389	0.451	71.932
makeTranscriptDb	0.192	0.020	0.212
makeTranscriptDbFromBiomart	3.091	0.156	19.393
makeTranscriptDbFromGFF	3.358	0.112	3.510
makeTranscriptDbFromUCSC	7.141	0.161	31.547
makeTxDbPackage	0.777	0.033	0.849
saveFeatures	0.003	0.007	0.010
select-methods	0.416	0.035	0.452
transcripts	1.140	0.025	1.166
transcriptsBy	3.188	0.023	3.221
transcriptsByOverlaps	0.434	0.010	0.444