Multiple platform build/check report for BioC 3.13 - CHECK results for AllelicImbalance on nebbiolo1

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### Running command:
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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:AllelicImbalance.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings AllelicImbalance_1.30.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/AllelicImbalance.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (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 ‘1.30.0’
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
lva                    120.906  0.916 121.830
import-bam              26.824  0.420  27.254
LinkVariantAlmlof-plot  26.926  0.302  27.230
getSnpIdFromLocation    20.406  1.724  22.133
* 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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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL AllelicImbalance
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 objects are masked from 'package:base':

    I, expand.grid, unname

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:grid':

    pattern

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 
 16.122   0.683  16.789

Example timings

name	user	system	elapsed
ASEset-barplot	0.429	0.008	0.436
ASEset-class	1.429	0.039	1.469
ASEset-filters	0.084	0.000	0.084
ASEset-gbarplot	0.061	0.003	0.066
ASEset-glocationplot	4.614	0.120	4.735
ASEset-gviztrack	0.561	0.080	0.641
ASEset-scanForHeterozygotes	1.680	0.028	1.708
ASEset.old	0.000	0.000	0.001
ASEset.sim	0.000	0.001	0.000
ASEsetFromBam	0.000	0.002	0.002
DetectedAI-class	0.187	0.008	0.195
DetectedAI-plot	1.424	0.016	1.440
DetectedAI-summary	0.223	0.007	0.231
GRvariants	0.002	0.000	0.002
GlobalAnalysis-class	0.001	0.000	0.001
LinkVariantAlmlof-class	0	0	0
LinkVariantAlmlof-plot	26.926	0.302	27.230
RegionSummary-class	0.000	0.001	0.001
RiskVariant-class	0.000	0.001	0.000
annotation-wrappers	3.845	0.322	4.167
annotationBarplot	0	0	0
barplot-lattice-support	0.164	0.000	0.164
binom.test	0.109	0.000	0.109
chisq.test	0.238	0.016	0.254
cigar-utilities	0.011	0.000	0.011
countAllelesFromBam	0.002	0.001	0.001
coverageMatrixListFromGAL	1.987	0.023	2.010
decorateWithExons	0.003	0.000	0.003
decorateWithGenes	0.002	0.000	0.002
defaultMapBias	0.043	0.004	0.047
defaultPhase	0.001	0.000	0.001
detectAI	0.188	0.000	0.188
fractionPlotDf	0.061	0.000	0.062
gba	0	0	0
genomatrix	0	0	0
genotype2phase	0.025	0.002	0.028
getAlleleCounts	3.633	0.056	3.688
getAlleleQuality	3.610	0.072	3.682
getAreaFromGeneNames	0.319	0.008	0.327
getDefaultMapBiasExpMean	0.041	0.000	0.041
getSnpIdFromLocation	20.406	1.724	22.133
histplot	0.000	0.000	0.001
implodeList-old	0.001	0.004	0.005
import-bam-2	0.012	0.000	0.011
import-bam	26.824	0.420	27.254
import-bcf	1.257	0.024	1.281
inferAlleles	0.018	0.000	0.019
inferAltAllele	0.029	0.000	0.028
inferGenotypes	0.058	0.000	0.057
initialize-ASEset	0.092	0.024	0.116
initialize-DetectedAI	0.188	0.000	0.188
initialize-GlobalAnalysis	0.004	0.000	0.005
initialize-RiskVariant	0.000	0.001	0.001
legendBarplot	0	0	0
locationplot	1.742	0.000	1.743
lva	120.906	0.916	121.830
lva.internal	0.702	0.028	0.730
makeMaskedFasta	1.289	0.000	1.289
mapBiasRef	0.038	0.000	0.039
minCountFilt	0.096	0.004	0.100
minFreqFilt	0.094	0.004	0.099
multiAllelicFilt	0.015	0.004	0.019
phase2genotype	0.037	0.004	0.041
phaseArray2phaseMatrix	0.019	0.004	0.023
phaseMatrix2Array	0.014	0.007	0.022
randomRef	0.028	0.004	0.032
reads	0	0	0
refAllele	0.020	0.004	0.024
regionSummary	1.227	0.028	1.254
scanForHeterozygotes-old	4.836	0.020	4.857

CHECK results for AllelicImbalance on nebbiolo1

Summary

Command output

Installation output

Tests output

Example timings