BioC 2.14: CHECK report for AllelicImbalance on zin2

Package: AllelicImbalance

Version: 1.2.0

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.2.0.tar.gz

StartedAt: 2014-10-07 21:38:46 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 21:44:24 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 338.5 seconds

RetCode: 0

Status:  OK

CheckDir: AllelicImbalance.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.2.0’
* 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 ... [19s/19s] 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 loading without being on the library search path ... 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 ... NOTE
  'BiocParallel' did not register default BiocParallelParams
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [133s/134s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
getAlleleCounts2     48.763  0.024  49.161
getSnpIdFromLocation 21.806  0.260  22.222
import-bam-functions 18.373  0.020  18.475
scanForHeterozygotes 15.497  0.004  15.530
getAlleleCounts      14.025  0.012  14.100
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [9s/9s]
 [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

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.14-bioc/meat/AllelicImbalance.Rcheck/00check.log’
for details.

* 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	0.384	0.000	0.385
ASEset-locationplot	0.684	0.004	0.688
ASEset	0.052	0.000	0.053
GRvariants	0.000	0.000	0.002
binom.test	0.064	0.004	0.069
chisq.test	0.048	0.000	0.049
cigar-utilities	0.036	0.000	0.033
decorateWithExons	0.000	0.000	0.002
decorateWithGenes	0.000	0.000	0.002
getAlleleCounts	14.025	0.012	14.100
getAlleleCounts2	48.763	0.024	49.161
getAnnotation-functions	3.160	0.052	3.219
getAreaFromGeneNames	0.444	0.016	0.461
getDefaultMapBiasExpMean	0.012	0.000	0.011
getSnpIdFromLocation	21.806	0.260	22.222
import-bam-functions	18.373	0.020	18.475
import-bcf-functions	0.416	0.000	0.417
initialize-ASEset	0.028	0.000	0.029
reads	0.004	0.000	0.001
scanForHeterozygotes	15.497	0.004	15.530