Package: AllelicImbalance

Version: 1.22.0

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_1.22.0.tar.gz

StartedAt: 2019-10-16 00:28:18 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 00:39:04 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 645.8 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 --install=check:AllelicImbalance.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AllelicImbalance_1.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.22.0’
* 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 44.777  4.108  49.369
import-bam           25.635  0.618  26.301
lva                  13.843  0.042  13.886
annotation-wrappers   6.023  0.600   6.624
ASEset-glocationplot  5.905  0.319   6.224
getAlleleCounts       6.065  0.033   6.097
getAlleleQuality      5.588  0.020   5.607
* 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/3.6/Resources/library’
* installing *source* package ‘AllelicImbalance’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (AllelicImbalance)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, 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, rowsum

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 | WARNINGS: 0 | FAILED: 0 ]
> 
> 
> 
> proc.time()
   user  system elapsed 
 25.038   1.908  26.901 

name	user	system	elapsed
ASEset-barplot	0.484	0.017	0.500
ASEset-class	1.808	0.076	1.884
ASEset-filters	0.137	0.005	0.142
ASEset-gbarplot	0.065	0.004	0.069
ASEset-glocationplot	5.905	0.319	6.224
ASEset-gviztrack	0.675	0.024	0.701
ASEset-scanForHeterozygotes	2.501	0.025	2.527
ASEset.old	0	0	0
ASEset.sim	0.000	0.001	0.001
ASEsetFromBam	0.003	0.004	0.007
DetectedAI-class	0.251	0.008	0.259
DetectedAI-plot	2.708	0.021	2.732
DetectedAI-summary	0.287	0.010	0.298
GRvariants	0.003	0.003	0.005
GlobalAnalysis-class	0.002	0.003	0.005
LinkVariantAlmlof-class	0	0	0
LinkVariantAlmlof-plot	2.566	0.009	2.577
RegionSummary-class	0.000	0.000	0.001
RiskVariant-class	0.001	0.000	0.000
annotation-wrappers	6.023	0.600	6.624
annotationBarplot	0.001	0.000	0.001
barplot-lattice-support	0.316	0.003	0.319
binom.test	0.165	0.004	0.169
chisq.test	0.361	0.009	0.371
cigar-utilities	0.020	0.002	0.022
countAllelesFromBam	0.003	0.004	0.008
coverageMatrixListFromGAL	1.132	0.040	1.172
decorateWithExons	0.002	0.003	0.005
decorateWithGenes	0.003	0.005	0.008
defaultMapBias	0.055	0.007	0.062
defaultPhase	0.002	0.001	0.003
detectAI	0.265	0.006	0.271
fractionPlotDf	0.077	0.004	0.080
gba	0.000	0.001	0.000
genomatrix	0.001	0.000	0.001
genotype2phase	0.065	0.008	0.072
getAlleleCounts	6.065	0.033	6.097
getAlleleQuality	5.588	0.020	5.607
getAreaFromGeneNames	0.482	0.016	0.497
getDefaultMapBiasExpMean	0.079	0.003	0.082
getSnpIdFromLocation	44.777	4.108	49.369
histplot	0.001	0.000	0.001
implodeList-old	0.012	0.000	0.012
import-bam-2	0.012	0.000	0.013
import-bam	25.635	0.618	26.301
import-bcf	1.177	0.049	1.226
inferAlleles	0.040	0.005	0.044
inferAltAllele	0.057	0.005	0.062
inferGenotypes	0.110	0.005	0.115
initialize-ASEset	0.073	0.000	0.074
initialize-DetectedAI	0.270	0.004	0.275
initialize-GlobalAnalysis	0.007	0.005	0.012
initialize-RiskVariant	0.004	0.005	0.007
legendBarplot	0.001	0.001	0.000
locationplot	2.660	0.050	2.711
lva	13.843	0.042	13.886
lva.internal	0.550	0.006	0.555
makeMaskedFasta	1.139	0.008	1.147
mapBiasRef	0.027	0.003	0.029
minCountFilt	0.188	0.003	0.191
minFreqFilt	0.220	0.005	0.225
multiAllelicFilt	0.034	0.003	0.038
phase2genotype	0.046	0.006	0.051
phaseArray2phaseMatrix	0.008	0.005	0.014
phaseMatrix2Array	0.006	0.003	0.009
randomRef	0.054	0.006	0.060
reads	0.000	0.000	0.001
refAllele	0.025	0.006	0.031
regionSummary	0.652	0.005	0.657
scanForHeterozygotes-old	4.787	0.082	4.870