BioC 2.14: CHECK report for AllelicImbalance on petty

Package: AllelicImbalance

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch AllelicImbalance_1.2.0.tar.gz

StartedAt: 2014-10-07 20:39:05 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 20:50:56 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 710.8 seconds

RetCode: 0

Status:  OK

CheckDir: AllelicImbalance.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch AllelicImbalance_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.2.0’
* 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 ... [39s/41s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [263s/265s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
getAlleleCounts2        99.958  0.157 100.241
import-bam-functions    36.024  0.636  36.704
getSnpIdFromLocation    33.271  1.105  34.410
scanForHeterozygotes    32.434  0.100  32.573
getAlleleCounts         28.384  0.068  28.481
getAnnotation-functions  7.003  0.612   8.777
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [20s/20s]
 [21s/21s] 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
  ‘/Users/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	0.662	0.004	0.667
ASEset-locationplot	1.311	0.024	1.338
ASEset	0.115	0.001	0.116
GRvariants	0.003	0.001	0.004
binom.test	0.140	0.001	0.141
chisq.test	0.098	0.002	0.098
cigar-utilities	0.074	0.001	0.075
decorateWithExons	0.003	0.001	0.003
decorateWithGenes	0.003	0.001	0.003
getAlleleCounts	28.384	0.068	28.481
getAlleleCounts2	99.958	0.157	100.241
getAnnotation-functions	7.003	0.612	8.777
getAreaFromGeneNames	1.116	0.039	1.158
getDefaultMapBiasExpMean	0.021	0.001	0.023
getSnpIdFromLocation	33.271	1.105	34.410
import-bam-functions	36.024	0.636	36.704
import-bcf-functions	0.835	0.045	0.881
initialize-ASEset	0.068	0.001	0.069
reads	0.001	0.000	0.002
scanForHeterozygotes	32.434	0.100	32.573