Package: Genominator

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Genominator_1.6.0.tar.gz

StartedAt: 2011-10-20 15:08:49 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 15:11:41 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 172.1 seconds

RetCode: 0

Status:  OK

CheckDir: Genominator.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/Genominator.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'Genominator/DESCRIPTION' ... OK
* this is package 'Genominator' version '1.6.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'Genominator' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    1.3Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 ... OK
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under inst/doc ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'plotting.pdf' from 754Kb to 171Kb
  consider running tools::compactPDF() on these files
* checking examples ... 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

* installing *source* package 'Genominator' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (Genominator)

name	user	system	elapsed
ExpData	0.001	0.000	0.001
addPrimingWeights	6.108	0.134	6.303
aggregateExpData	1.487	0.025	1.547
applyMapped	1.860	0.104	1.981
collapseExpData	3.342	0.165	3.604
computeCoverage	1.094	0.057	1.202
computePrimingWeights	0.494	0.046	0.542
getRegion	0.216	0.004	0.222
importFromAlignedReads	0.000	0.001	0.001
importToExpData	0.493	0.013	0.528
joinExpData	3.996	0.069	4.134
makeGeneRepresentation	0.458	0.006	0.467
mergeWithAnnotation	0.433	0.006	0.441
plot.genominator.coverage	3.357	0.138	3.539
plot.genominator.goodness.of.fit	0.873	0.068	0.954
regionGoodnessOfFit-methods	0.788	0.057	0.860
splitByAnnotation	0.850	0.014	0.868
summarizeByAnnotation	0.434	0.007	0.443
summarizeExpData	0.616	0.014	0.637
validAnnotation	0.026	0.002	0.028
yeastAnno	0.332	0.014	0.346