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 4.0.5 (2021-03-31)
* 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     20.683  1.156  21.873
import-bam               20.801  0.276  21.120
lva                      13.446  0.044  13.511
scanForHeterozygotes-old  6.192  0.016   6.214
annotation-wrappers       5.441  0.238   5.688
getAlleleCounts           5.523  0.024   5.554
* 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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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 
 21.345   0.889  23.624

Example timings

name	user	system	elapsed
ASEset-barplot	0.298	0.020	0.318
ASEset-class	0.549	0.027	0.578
ASEset-filters	0.066	0.002	0.068
ASEset-gbarplot	0.050	0.002	0.052
ASEset-glocationplot	4.410	0.074	4.490
ASEset-gviztrack	0.740	0.065	0.806
ASEset-scanForHeterozygotes	2.316	0.025	2.350
ASEset.old	0.000	0.001	0.000
ASEset.sim	0.001	0.000	0.000
ASEsetFromBam	0.001	0.002	0.003
DetectedAI-class	0.120	0.002	0.122
DetectedAI-plot	1.664	0.015	1.680
DetectedAI-summary	0.139	0.008	0.147
GRvariants	0.001	0.002	0.003
GlobalAnalysis-class	0.001	0.002	0.003
LinkVariantAlmlof-class	0	0	0
LinkVariantAlmlof-plot	2.988	0.012	3.005
RegionSummary-class	0.000	0.000	0.001
RiskVariant-class	0.001	0.000	0.001
annotation-wrappers	5.441	0.238	5.688
annotationBarplot	0.000	0.000	0.001
barplot-lattice-support	0.190	0.002	0.194
binom.test	0.087	0.002	0.089
chisq.test	0.231	0.004	0.236
cigar-utilities	0.014	0.001	0.015
countAllelesFromBam	0.002	0.003	0.004
coverageMatrixListFromGAL	1.031	0.023	1.056
decorateWithExons	0.002	0.003	0.005
decorateWithGenes	0.002	0.003	0.004
defaultMapBias	0.047	0.008	0.055
defaultPhase	0.001	0.001	0.002
detectAI	0.201	0.009	0.210
fractionPlotDf	0.045	0.003	0.049
gba	0.000	0.001	0.000
genomatrix	0.000	0.000	0.001
genotype2phase	0.049	0.005	0.054
getAlleleCounts	5.523	0.024	5.554
getAlleleQuality	4.660	0.015	4.678
getAreaFromGeneNames	0.390	0.007	0.398
getDefaultMapBiasExpMean	0.036	0.003	0.038
getSnpIdFromLocation	20.683	1.156	21.873
histplot	0.000	0.001	0.000
implodeList-old	0.006	0.000	0.007
import-bam-2	0.009	0.000	0.009
import-bam	20.801	0.276	21.120
import-bcf	1.083	0.018	1.103
inferAlleles	0.015	0.002	0.017
inferAltAllele	0.022	0.002	0.025
inferGenotypes	0.043	0.002	0.045
initialize-ASEset	0.091	0.001	0.092
initialize-DetectedAI	0.118	0.002	0.120
initialize-GlobalAnalysis	0.005	0.002	0.007
initialize-RiskVariant	0.002	0.003	0.006
legendBarplot	0	0	0
locationplot	2.214	0.038	2.256
lva	13.446	0.044	13.511
lva.internal	0.440	0.004	0.444
makeMaskedFasta	0.958	0.006	0.966
mapBiasRef	0.027	0.003	0.030
minCountFilt	0.102	0.003	0.106
minFreqFilt	0.087	0.002	0.089
multiAllelicFilt	0.015	0.003	0.017
phase2genotype	0.027	0.003	0.032
phaseArray2phaseMatrix	0.009	0.002	0.011
phaseMatrix2Array	0.008	0.002	0.010
randomRef	0.023	0.002	0.025
reads	0	0	0
refAllele	0.018	0.003	0.021
regionSummary	0.797	0.005	0.803
scanForHeterozygotes-old	6.192	0.016	6.214

CHECK report for AllelicImbalance on merida1

Summary

Command output

Installation output

Tests output

Example timings