Multiple platform build/check report for BioC 3.14 - CHECK results for AllelicImbalance on machv2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AllelicImbalance.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AllelicImbalance_1.32.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/AllelicImbalance.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.32.0’
* 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 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
lva                      151.911  0.285 152.341
LinkVariantAlmlof-plot    31.773  0.121  31.935
getSnpIdFromLocation      29.902  1.636  31.559
import-bam                26.068  0.334  26.483
scanForHeterozygotes-old   9.888  0.037   9.940
annotation-wrappers        6.728  0.260   7.014
ASEset-glocationplot       6.716  0.128   6.853
getAlleleQuality           6.795  0.033   6.916
getAlleleCounts            6.528  0.026   6.561
* 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/Resources/bin/R CMD INSTALL AllelicImbalance
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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

Attaching package: 'BiocGenerics'

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
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 96 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 96 ]
> 
> 
> 
> proc.time()
   user  system elapsed 
 26.866   1.141  28.022

Example timings

name	user	system	elapsed
ASEset-barplot	0.509	0.048	0.558
ASEset-class	1.047	0.011	1.060
ASEset-filters	0.176	0.005	0.185
ASEset-gbarplot	0.133	0.014	0.147
ASEset-glocationplot	6.716	0.128	6.853
ASEset-gviztrack	1.026	0.042	1.068
ASEset-scanForHeterozygotes	3.175	0.027	3.206
ASEset.old	0.000	0.001	0.000
ASEset.sim	0.000	0.001	0.000
ASEsetFromBam	0.002	0.003	0.005
DetectedAI-class	0.420	0.006	0.427
DetectedAI-plot	2.863	0.026	2.894
DetectedAI-summary	0.497	0.016	0.514
GRvariants	0.002	0.004	0.005
GlobalAnalysis-class	0.002	0.003	0.005
LinkVariantAlmlof-class	0	0	0
LinkVariantAlmlof-plot	31.773	0.121	31.935
RegionSummary-class	0.001	0.000	0.001
RiskVariant-class	0	0	0
annotation-wrappers	6.728	0.260	7.014
annotationBarplot	0.000	0.000	0.001
barplot-lattice-support	0.319	0.002	0.322
binom.test	0.223	0.004	0.227
chisq.test	0.434	0.005	0.438
cigar-utilities	0.020	0.001	0.021
countAllelesFromBam	0.002	0.004	0.006
coverageMatrixListFromGAL	2.782	0.023	2.806
decorateWithExons	0.002	0.004	0.005
decorateWithGenes	0.002	0.003	0.004
defaultMapBias	0.069	0.006	0.075
defaultPhase	0.001	0.001	0.002
detectAI	0.434	0.004	0.438
fractionPlotDf	0.097	0.004	0.101
gba	0.000	0.001	0.001
genomatrix	0	0	0
genotype2phase	0.059	0.007	0.067
getAlleleCounts	6.528	0.026	6.561
getAlleleQuality	6.795	0.033	6.916
getAreaFromGeneNames	0.63	0.01	0.64
getDefaultMapBiasExpMean	0.091	0.004	0.094
getSnpIdFromLocation	29.902	1.636	31.559
histplot	0.000	0.000	0.001
implodeList-old	0.010	0.001	0.010
import-bam-2	0.020	0.001	0.020
import-bam	26.068	0.334	26.483
import-bcf	1.354	0.028	1.424
inferAlleles	0.033	0.003	0.036
inferAltAllele	0.042	0.003	0.044
inferGenotypes	0.115	0.004	0.120
initialize-ASEset	0.219	0.001	0.221
initialize-DetectedAI	0.413	0.004	0.417
initialize-GlobalAnalysis	0.007	0.003	0.010
initialize-RiskVariant	0.002	0.003	0.005
legendBarplot	0.000	0.000	0.001
locationplot	3.552	0.057	3.620
lva	151.911	0.285	152.341
lva.internal	1.155	0.007	1.161
makeMaskedFasta	1.069	0.012	1.081
mapBiasRef	0.056	0.003	0.059
minCountFilt	0.185	0.006	0.192
minFreqFilt	0.177	0.004	0.181
multiAllelicFilt	0.031	0.005	0.036
phase2genotype	0.063	0.005	0.067
phaseArray2phaseMatrix	0.042	0.005	0.046
phaseMatrix2Array	0.035	0.004	0.037
randomRef	0.050	0.004	0.053
reads	0.000	0.000	0.001
refAllele	0.032	0.005	0.037
regionSummary	2.220	0.030	2.258
scanForHeterozygotes-old	9.888	0.037	9.940

CHECK results for AllelicImbalance on machv2

Summary

Command output

Installation output

Tests output

Example timings