Package: Genominator

Version: 1.12.0

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings Genominator_1.12.0.tar.gz

StartedAt: 2013-03-25 01:30:33 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:33:21 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 167.8 seconds

RetCode: 0

Status:  OK

CheckDir: Genominator.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/Genominator.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Genominator/DESCRIPTION’ ... OK
* this is package ‘Genominator’ version ‘1.12.0’
* 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 whether package ‘Genominator’ can be installed ... OK
* checking installed package size ... OK
* 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 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 ... 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
joinExpData       7.572  0.064   7.664
addPrimingWeights 6.356  0.132   6.681
* 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
** installing vignettes
   ‘Genominator.Rnw’ 
   ‘plotting.Rnw’ 
   ‘withShortRead.Rnw’ 
** testing if installed package can be loaded

* DONE (Genominator)

name	user	system	elapsed
ExpData	0.000	0.000	0.002
addPrimingWeights	6.356	0.132	6.681
aggregateExpData	3.012	0.008	3.023
applyMapped	2.369	0.004	2.599
collapseExpData	3.252	0.024	3.328
computeCoverage	1.588	0.020	1.689
computePrimingWeights	0.336	0.036	0.411
getRegion	0.440	0.000	0.447
importFromAlignedReads	0	0	0
importToExpData	0.884	0.004	0.901
joinExpData	7.572	0.064	7.664
makeGeneRepresentation	0.284	0.008	0.292
mergeWithAnnotation	0.856	0.020	1.010
plot.genominator.coverage	4.689	0.036	4.935
plot.genominator.goodness.of.fit	1.104	0.012	1.190
regionGoodnessOfFit-methods	1.040	0.016	1.152
splitByAnnotation	1.712	0.008	1.839
summarizeByAnnotation	0.828	0.000	0.845
summarizeExpData	0.920	0.008	0.927
validAnnotation	0.016	0.004	0.018
yeastAnno	0.152	0.012	0.165