BioC 2.13: CHECK report for AllelicImbalance on perceval

Package: AllelicImbalance

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch AllelicImbalance_1.0.0.tar.gz

StartedAt: 2014-04-04 23:18:59 -0700 (Fri, 04 Apr 2014)

EndedAt: 2014-04-04 23:27:28 -0700 (Fri, 04 Apr 2014)

EllapsedTime: 509.0 seconds

RetCode: 0

Status:  OK

CheckDir: AllelicImbalance.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AllelicImbalance/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AllelicImbalance’ version ‘1.0.0’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘AllelicImbalance’ can be installed ... [28s/29s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [192s/194s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
getAlleleCount          70.503  0.368  71.725
getSnpIdFromLocation    42.547  1.559  44.208
import-bam-functions    28.881  0.754  29.701
scanForHeterozygotes    22.157  0.167  22.384
getAnnotation-functions  7.062  0.298   7.429
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [16s/16s]
 [16s/16s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘AllelicImbalance’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (AllelicImbalance)

name	user	system	elapsed
ASEset-barplot	0.652	0.018	0.688
ASEset-locationplot	0.602	0.013	0.627
ASEset	0.100	0.006	0.109
GRvariants	0.014	0.001	0.016
binom.test	0.603	0.004	0.612
chisq.test	0.076	0.006	0.082
cigar-utilities	0.060	0.005	0.066
decorateWithExons	0.010	0.003	0.013
decorateWithGenes	0.009	0.002	0.012
getAlleleCount	70.503	0.368	71.725
getAnnotation-functions	7.062	0.298	7.429
getAreaFromGeneNames	0.663	0.045	0.719
getDefaultMapBiasExpMean	0.029	0.004	0.034
getSnpIdFromLocation	42.547	1.559	44.208
import-bam-functions	28.881	0.754	29.701
import-bcf-functions	0.677	0.044	0.721
initialize-ASEset	0.047	0.016	0.063
reads	0.002	0.003	0.006
scanForHeterozygotes	22.157	0.167	22.384