BioC 2.13: CHECK report for AllelicImbalance on zin1

Package: AllelicImbalance

Version: 1.0.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.0.0.tar.gz

StartedAt: 2014-04-04 23:25:32 -0700 (Fri, 04 Apr 2014)

EndedAt: 2014-04-04 23:30:25 -0700 (Fri, 04 Apr 2014)

EllapsedTime: 292.9 seconds

RetCode: 0

Status:  OK

CheckDir: AllelicImbalance.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (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 ... [16s/16s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [123s/123s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
getAlleleCount       49.379  0.028  49.552
getSnpIdFromLocation 26.034  0.384  26.464
import-bam-functions 17.173  0.008  17.205
scanForHeterozygotes 15.701  0.000  15.729
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [8s/8s]
 [9s/9s] 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	0.368	0.000	0.366
ASEset-locationplot	0.428	0.008	0.437
ASEset	0.064	0.000	0.063
GRvariants	0.000	0.004	0.005
binom.test	0.072	0.000	0.072
chisq.test	0.056	0.000	0.054
cigar-utilities	0.044	0.000	0.044
decorateWithExons	0.004	0.000	0.003
decorateWithGenes	0.004	0.000	0.003
getAlleleCount	49.379	0.028	49.552
getAnnotation-functions	3.816	0.044	3.869
getAreaFromGeneNames	0.404	0.008	0.410
getDefaultMapBiasExpMean	0.024	0.000	0.022
getSnpIdFromLocation	26.034	0.384	26.464
import-bam-functions	17.173	0.008	17.205
import-bcf-functions	0.384	0.000	0.384
initialize-ASEset	0.032	0.000	0.031
reads	0	0	0
scanForHeterozygotes	15.701	0.000	15.729