Multiple platform build/check report for BioC 3.12 - CHECK report for AllelicImbalance on merida1

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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_1.28.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/AllelicImbalance.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.28.0’
* 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 (user + system) or elapsed time > 5s
                           user system elapsed
getSnpIdFromLocation     24.418  1.508  26.087
import-bam               23.439  0.363  23.860
lva                      16.132  0.049  16.203
scanForHeterozygotes-old  7.942  0.043   7.995
annotation-wrappers       6.647  0.271   6.948
getAlleleCounts           6.046  0.060   6.114
getAlleleQuality          5.448  0.026   5.481
ASEset-glocationplot      5.359  0.086   5.462
* 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

Installation output

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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/4.0/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)

Tests output


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.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: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

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")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

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

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: Rsamtools
══ Skipped tests ═══════════════════════════════════════════════════════════════
● empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 96 ]
> 
> 
> 
> proc.time()
   user  system elapsed 
 23.860   0.980  26.221

Example timings

name	user	system	elapsed
ASEset-barplot	0.378	0.007	0.386
ASEset-class	0.675	0.056	0.732
ASEset-filters	0.081	0.011	0.091
ASEset-gbarplot	0.075	0.012	0.087
ASEset-glocationplot	5.359	0.086	5.462
ASEset-gviztrack	0.937	0.078	1.018
ASEset-scanForHeterozygotes	2.541	0.021	2.573
ASEset.old	0	0	0
ASEset.sim	0	0	0
ASEsetFromBam	0.001	0.002	0.003
DetectedAI-class	0.144	0.003	0.147
DetectedAI-plot	1.809	0.016	1.832
DetectedAI-summary	0.184	0.010	0.194
GRvariants	0.002	0.002	0.005
GlobalAnalysis-class	0.002	0.004	0.005
LinkVariantAlmlof-class	0.001	0.001	0.001
LinkVariantAlmlof-plot	3.536	0.019	3.561
RegionSummary-class	0.001	0.000	0.000
RiskVariant-class	0.001	0.000	0.000
annotation-wrappers	6.647	0.271	6.948
annotationBarplot	0.000	0.001	0.000
barplot-lattice-support	0.169	0.002	0.172
binom.test	0.079	0.003	0.083
chisq.test	0.240	0.004	0.244
cigar-utilities	0.017	0.001	0.017
countAllelesFromBam	0.002	0.003	0.004
coverageMatrixListFromGAL	1.126	0.012	1.140
decorateWithExons	0.002	0.003	0.004
decorateWithGenes	0.002	0.003	0.004
defaultMapBias	0.059	0.005	0.064
defaultPhase	0.001	0.000	0.002
detectAI	0.151	0.003	0.155
fractionPlotDf	0.042	0.002	0.044
gba	0.000	0.000	0.001
genomatrix	0.000	0.000	0.001
genotype2phase	0.037	0.004	0.041
getAlleleCounts	6.046	0.060	6.114
getAlleleQuality	5.448	0.026	5.481
getAreaFromGeneNames	0.435	0.009	0.445
getDefaultMapBiasExpMean	0.039	0.003	0.043
getSnpIdFromLocation	24.418	1.508	26.087
histplot	0	0	0
implodeList-old	0.007	0.001	0.008
import-bam-2	0.015	0.001	0.016
import-bam	23.439	0.363	23.860
import-bcf	1.129	0.027	1.158
inferAlleles	0.024	0.002	0.026
inferAltAllele	0.033	0.003	0.036
inferGenotypes	0.067	0.004	0.070
initialize-ASEset	0.111	0.001	0.112
initialize-DetectedAI	0.158	0.004	0.162
initialize-GlobalAnalysis	0.007	0.002	0.010
initialize-RiskVariant	0.001	0.003	0.005
legendBarplot	0.001	0.001	0.001
locationplot	2.573	0.025	2.601
lva	16.132	0.049	16.203
lva.internal	0.557	0.009	0.570
makeMaskedFasta	1.083	0.015	1.103
mapBiasRef	0.032	0.004	0.037
minCountFilt	0.127	0.005	0.133
minFreqFilt	0.127	0.004	0.132
multiAllelicFilt	0.021	0.004	0.025
phase2genotype	0.040	0.004	0.044
phaseArray2phaseMatrix	0.012	0.003	0.014
phaseMatrix2Array	0.011	0.004	0.015
randomRef	0.034	0.003	0.037
reads	0.000	0.001	0.000
refAllele	0.028	0.004	0.033
regionSummary	1.005	0.011	1.019
scanForHeterozygotes-old	7.942	0.043	7.995

CHECK report for AllelicImbalance on merida1

Summary

Command output

Installation output

Tests output

Example timings