Package: AllelicImbalance

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.16.0.tar.gz

StartedAt: 2018-04-12 00:15:58 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 00:23:10 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 432.5 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 AllelicImbalance_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.16.0’
* package encoding: UTF-8
* 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 ... 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
getSnpIdFromLocation 20.328  1.525  22.189
import-bam           13.808  0.340  14.394
annotation-wrappers   7.789  0.228   8.159
lva                   6.101  0.017   6.224
ASEset-glocationplot  5.657  0.023   5.789
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 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
* DONE

Status: OK

* installing *source* package ‘AllelicImbalance’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for 'chisq.test' from package 'stats' in package 'AllelicImbalance'
Creating a generic function for 'binom.test' from package 'stats' in package 'AllelicImbalance'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (AllelicImbalance)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> test_check("AllelicImbalance")
Loading required package: AllelicImbalance
Loading required package: grid
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following object is masked from 'package:base':

    apply

Loading required package: GenomicAlignments
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:DelayedArray':

    type

The following object is masked from 'package:base':

    strsplit

Loading required package: Rsamtools
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 96 SKIPPED: 1 FAILED: 0
> 
> 
> 
> proc.time()
   user  system elapsed 
 17.497   0.495  18.541 

name	user	system	elapsed
ASEset-barplot	1.023	0.006	1.046
ASEset-class	0.819	0.044	0.873
ASEset-filters	0.115	0.004	0.118
ASEset-gbarplot	0.033	0.002	0.035
ASEset-glocationplot	5.657	0.023	5.789
ASEset-gviztrack	0.864	0.047	0.918
ASEset-scanForHeterozygotes	2.334	0.027	2.395
ASEset.old	0.001	0.000	0.001
ASEset.sim	0.001	0.000	0.001
ASEsetFromBam	0.002	0.001	0.003
DetectedAI-class	0.065	0.001	0.070
DetectedAI-plot	1.97	0.01	2.00
DetectedAI-summary	0.110	0.005	0.115
GRvariants	0.002	0.002	0.004
GlobalAnalysis-class	0.002	0.001	0.003
LinkVariantAlmlof-class	0.000	0.000	0.001
LinkVariantAlmlof-plot	1.788	0.005	1.820
RegionSummary-class	0.001	0.000	0.000
RiskVariant-class	0.001	0.000	0.000
annotation-wrappers	7.789	0.228	8.159
annotationBarplot	0.001	0.000	0.000
barplot-lattice-support	0.172	0.001	0.184
binom.test	0.033	0.002	0.034
chisq.test	0.082	0.002	0.084
cigar-utilities	0.014	0.001	0.014
countAllelesFromBam	0.003	0.002	0.005
coverageMatrixListFromGAL	1.001	0.027	1.048
decorateWithExons	0.003	0.001	0.004
decorateWithGenes	0.003	0.001	0.004
defaultMapBias	0.053	0.003	0.055
defaultPhase	0.001	0.000	0.002
detectAI	0.060	0.002	0.062
fractionPlotDf	0.030	0.002	0.032
gba	0.000	0.000	0.001
genomatrix	0.000	0.000	0.001
genotype2phase	0.038	0.004	0.043
getAlleleCounts	4.576	0.018	4.654
getAlleleQuality	4.558	0.014	4.653
getAreaFromGeneNames	0.402	0.010	0.414
getDefaultMapBiasExpMean	0.027	0.002	0.029
getSnpIdFromLocation	20.328	1.525	22.189
histplot	0.001	0.000	0.000
implodeList-old	0.008	0.000	0.008
import-bam-2	0.009	0.000	0.009
import-bam	13.808	0.340	14.394
import-bcf	0.647	0.024	0.680
inferAlleles	0.086	0.001	0.089
inferAltAllele	0.015	0.001	0.017
inferGenotypes	0.086	0.002	0.093
initialize-ASEset	0.221	0.001	0.234
initialize-DetectedAI	0.055	0.002	0.056
initialize-GlobalAnalysis	0.006	0.002	0.008
initialize-RiskVariant	0.002	0.002	0.004
legendBarplot	0.001	0.001	0.001
locationplot	1.759	0.017	1.810
lva	6.101	0.017	6.224
lva.internal	0.788	0.004	0.802
makeMaskedFasta	0.585	0.004	0.599
mapBiasRef	0.012	0.002	0.014
minCountFilt	0.035	0.002	0.043
minFreqFilt	0.033	0.002	0.036
multiAllelicFilt	0.010	0.002	0.012
phase2genotype	0.015	0.002	0.017
phaseArray2phaseMatrix	0.006	0.001	0.007
phaseMatrix2Array	0.008	0.002	0.009
randomRef	0.012	0.001	0.014
reads	0	0	0
refAllele	0.015	0.001	0.016
regionSummary	0.422	0.004	0.438
scanForHeterozygotes-old	4.490	0.020	4.598