Package: AllelicImbalance

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AllelicImbalance.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AllelicImbalance_1.20.0.tar.gz

StartedAt: 2019-04-15 22:19:07 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 22:26:51 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 464.0 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 --install=check:AllelicImbalance.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AllelicImbalance_1.20.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.20.0’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
getSnpIdFromLocation 24.518  1.816  26.574
import-bam           20.460  0.420  21.087
lva                  10.156  0.032  10.294
annotation-wrappers   5.242  0.248   5.523
* 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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL AllelicImbalance
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘AllelicImbalance’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare 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 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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, basename, cbind, colMeans, colSums, colnames,
    dirname, 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

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, 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 
 18.721   0.859  19.748 

name	user	system	elapsed
ASEset-barplot	0.336	0.009	0.346
ASEset-class	0.699	0.092	0.799
ASEset-filters	0.108	0.002	0.110
ASEset-gbarplot	0.094	0.003	0.097
ASEset-glocationplot	4.551	0.039	4.626
ASEset-gviztrack	0.599	0.008	0.614
ASEset-scanForHeterozygotes	1.972	0.014	1.995
ASEset.old	0	0	0
ASEset.sim	0.000	0.000	0.001
ASEsetFromBam	0.003	0.002	0.005
DetectedAI-class	0.220	0.003	0.224
DetectedAI-plot	2.044	0.020	2.084
DetectedAI-summary	0.198	0.005	0.205
GRvariants	0.001	0.001	0.003
GlobalAnalysis-class	0.002	0.002	0.003
LinkVariantAlmlof-class	0.000	0.000	0.001
LinkVariantAlmlof-plot	2.183	0.008	2.207
RegionSummary-class	0.001	0.000	0.000
RiskVariant-class	0.001	0.000	0.000
annotation-wrappers	5.242	0.248	5.523
annotationBarplot	0.000	0.001	0.000
barplot-lattice-support	0.216	0.001	0.222
binom.test	0.091	0.002	0.093
chisq.test	0.242	0.002	0.245
cigar-utilities	0.01	0.00	0.01
countAllelesFromBam	0.001	0.001	0.003
coverageMatrixListFromGAL	0.993	0.004	1.006
decorateWithExons	0.002	0.001	0.003
decorateWithGenes	0.002	0.002	0.005
defaultMapBias	0.035	0.002	0.039
defaultPhase	0.001	0.000	0.002
detectAI	0.187	0.002	0.190
fractionPlotDf	0.061	0.002	0.062
gba	0	0	0
genomatrix	0.000	0.000	0.001
genotype2phase	0.039	0.003	0.042
getAlleleCounts	4.743	0.017	4.794
getAlleleQuality	4.628	0.014	4.687
getAreaFromGeneNames	0.394	0.007	0.405
getDefaultMapBiasExpMean	0.055	0.001	0.058
getSnpIdFromLocation	24.518	1.816	26.574
histplot	0	0	0
implodeList-old	0.006	0.001	0.006
import-bam-2	0.011	0.000	0.011
import-bam	20.460	0.420	21.087
import-bcf	1.000	0.027	1.046
inferAlleles	0.041	0.002	0.046
inferAltAllele	0.050	0.001	0.052
inferGenotypes	0.089	0.003	0.095
initialize-ASEset	0.075	0.001	0.077
initialize-DetectedAI	0.168	0.002	0.174
initialize-GlobalAnalysis	0.005	0.001	0.006
initialize-RiskVariant	0.001	0.001	0.003
legendBarplot	0.001	0.000	0.001
locationplot	2.639	0.145	2.811
lva	10.156	0.032	10.294
lva.internal	0.397	0.004	0.404
makeMaskedFasta	0.927	0.004	0.935
mapBiasRef	0.021	0.003	0.024
minCountFilt	0.166	0.002	0.170
minFreqFilt	0.142	0.003	0.148
multiAllelicFilt	0.040	0.003	0.045
phase2genotype	0.051	0.005	0.057
phaseArray2phaseMatrix	0.010	0.003	0.012
phaseMatrix2Array	0.006	0.002	0.009
randomRef	0.045	0.002	0.046
reads	0	0	0
refAllele	0.013	0.002	0.014
regionSummary	0.721	0.002	0.730
scanForHeterozygotes-old	4.297	0.023	4.365