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     22.887  1.154  24.140
import-bam               22.168  0.343  22.557
lva                      14.504  0.041  14.563
scanForHeterozygotes-old  6.719  0.024   6.748
annotation-wrappers       5.678  0.243   5.929
getAlleleCounts           5.738  0.083   5.882
getAlleleQuality          5.655  0.021   5.681
* 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 
 21.852   0.913  24.067

Example timings

name	user	system	elapsed
ASEset-barplot	0.310	0.007	0.318
ASEset-class	0.558	0.053	0.614
ASEset-filters	0.069	0.002	0.071
ASEset-gbarplot	0.048	0.002	0.050
ASEset-glocationplot	4.672	0.075	4.764
ASEset-gviztrack	0.797	0.062	0.862
ASEset-scanForHeterozygotes	2.477	0.023	2.510
ASEset.old	0.000	0.001	0.001
ASEset.sim	0	0	0
ASEsetFromBam	0.003	0.004	0.006
DetectedAI-class	0.149	0.003	0.153
DetectedAI-plot	1.790	0.018	1.813
DetectedAI-summary	0.186	0.013	0.198
GRvariants	0.002	0.003	0.005
GlobalAnalysis-class	0.001	0.002	0.003
LinkVariantAlmlof-class	0.000	0.001	0.001
LinkVariantAlmlof-plot	3.163	0.013	3.179
RegionSummary-class	0.000	0.000	0.001
RiskVariant-class	0	0	0
annotation-wrappers	5.678	0.243	5.929
annotationBarplot	0.000	0.001	0.000
barplot-lattice-support	0.184	0.002	0.187
binom.test	0.098	0.002	0.101
chisq.test	0.236	0.003	0.239
cigar-utilities	0.018	0.001	0.019
countAllelesFromBam	0.002	0.004	0.005
coverageMatrixListFromGAL	1.194	0.017	1.211
decorateWithExons	0.002	0.003	0.005
decorateWithGenes	0.001	0.001	0.003
defaultMapBias	0.049	0.004	0.054
defaultPhase	0.001	0.001	0.001
detectAI	0.152	0.004	0.157
fractionPlotDf	0.049	0.002	0.050
gba	0.000	0.000	0.001
genomatrix	0	0	0
genotype2phase	0.038	0.004	0.042
getAlleleCounts	5.738	0.083	5.882
getAlleleQuality	5.655	0.021	5.681
getAreaFromGeneNames	0.379	0.005	0.385
getDefaultMapBiasExpMean	0.036	0.002	0.038
getSnpIdFromLocation	22.887	1.154	24.140
histplot	0	0	0
implodeList-old	0.008	0.000	0.009
import-bam-2	0.015	0.001	0.016
import-bam	22.168	0.343	22.557
import-bcf	1.114	0.020	1.135
inferAlleles	0.022	0.003	0.025
inferAltAllele	0.029	0.003	0.032
inferGenotypes	0.059	0.004	0.063
initialize-ASEset	0.098	0.001	0.099
initialize-DetectedAI	0.116	0.002	0.117
initialize-GlobalAnalysis	0.004	0.002	0.006
initialize-RiskVariant	0.002	0.002	0.003
legendBarplot	0	0	0
locationplot	1.948	0.034	1.986
lva	14.504	0.041	14.563
lva.internal	0.556	0.005	0.562
makeMaskedFasta	0.979	0.017	0.997
mapBiasRef	0.020	0.002	0.023
minCountFilt	0.081	0.002	0.084
minFreqFilt	0.082	0.002	0.084
multiAllelicFilt	0.016	0.003	0.018
phase2genotype	0.028	0.003	0.033
phaseArray2phaseMatrix	0.014	0.004	0.018
phaseMatrix2Array	0.009	0.003	0.011
randomRef	0.031	0.003	0.034
reads	0.001	0.000	0.000
refAllele	0.025	0.003	0.029
regionSummary	0.848	0.009	0.859
scanForHeterozygotes-old	6.719	0.024	6.748

CHECK report for AllelicImbalance on merida1

Summary

Command output

Installation output

Tests output

Example timings