BioC 2.14: CHECK report for AllelicImbalance on morelia

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 21:07:02 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 21:13:43 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 401.3 seconds

RetCode: 0

Status:  OK

CheckDir: AllelicImbalance.Rcheck

Warnings: 0

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


* 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-darwin13.1.0 (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 ... [22s/22s] 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 ... [152s/152s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
getAlleleCounts2     53.310  0.104  53.442
getSnpIdFromLocation 23.315  0.582  23.930
import-bam-functions 20.115  0.615  20.742
scanForHeterozygotes 19.045  0.080  19.138
getAlleleCounts      17.318  0.053  17.413
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [11s/11s]
 [11s/11s] 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	0.451	0.002	0.454
ASEset-locationplot	0.765	0.015	0.781
ASEset	0.063	0.000	0.064
GRvariants	0.002	0.000	0.003
binom.test	0.087	0.001	0.089
chisq.test	0.054	0.001	0.056
cigar-utilities	0.044	0.000	0.046
decorateWithExons	0.001	0.001	0.002
decorateWithGenes	0.002	0.000	0.002
getAlleleCounts	17.318	0.053	17.413
getAlleleCounts2	53.310	0.104	53.442
getAnnotation-functions	3.456	0.131	3.642
getAreaFromGeneNames	0.553	0.021	0.574
getDefaultMapBiasExpMean	0.011	0.001	0.012
getSnpIdFromLocation	23.315	0.582	23.930
import-bam-functions	20.115	0.615	20.742
import-bcf-functions	0.414	0.021	0.435
initialize-ASEset	0.039	0.001	0.040
reads	0.000	0.000	0.001
scanForHeterozygotes	19.045	0.080	19.138