Mac ARM64 build report for BioC 3.18 - CHECK results for AllelicImbalance on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson1	macOS 13.6.1 Ventura	arm64	4.3.3 (2024-02-29) -- "Angel Food Cake"	4376
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_1.40.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/AllelicImbalance.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AllelicImbalance/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AllelicImbalance’ version ‘1.40.0’
* 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    CHANGES IN VERSION 1.12.0
* 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
import-bam           32.670  0.241  33.616
getSnpIdFromLocation 24.056  1.072  25.644
lva                   8.679  0.033   8.712
annotation-wrappers   6.768  0.237   7.035
ASEset-glocationplot  5.540  0.060   5.604
getAlleleCounts       5.445  0.050   5.510
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/AllelicImbalance.Rcheck/00check.log’
for details.

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/4.3-arm64/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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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, aperm, 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:utils':

    findMatches

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 (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_utils.R:3:1'

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 96 ]
> 
> 
> 
> proc.time()
   user  system elapsed 
 22.473   0.904  23.437

Example timings

name	user	system	elapsed
ASEset-barplot	0.219	0.007	0.226
ASEset-class	0.440	0.018	0.458
ASEset-filters	0.053	0.007	0.060
ASEset-gbarplot	0.041	0.007	0.048
ASEset-glocationplot	5.540	0.060	5.604
ASEset-gviztrack	0.656	0.048	0.704
ASEset-scanForHeterozygotes	1.809	0.046	1.857
ASEset.old	0	0	0
ASEset.sim	0	0	0
ASEsetFromBam	0.001	0.003	0.004
DetectedAI-class	0.090	0.004	0.094
DetectedAI-plot	1.286	0.020	1.310
DetectedAI-summary	0.104	0.009	0.113
GRvariants	0.002	0.003	0.004
GlobalAnalysis-class	0.001	0.003	0.003
LinkVariantAlmlof-class	0	0	0
LinkVariantAlmlof-plot	2.072	0.015	2.092
RegionSummary-class	0	0	0
RiskVariant-class	0.000	0.000	0.001
annotation-wrappers	6.768	0.237	7.035
annotationBarplot	0	0	0
barplot-lattice-support	0.109	0.002	0.112
binom.test	0.043	0.003	0.046
chisq.test	0.122	0.004	0.128
cigar-utilities	0.014	0.001	0.015
countAllelesFromBam	0.001	0.003	0.004
coverageMatrixListFromGAL	0.814	0.050	0.869
decorateWithExons	0.001	0.003	0.004
decorateWithGenes	0.002	0.002	0.004
defaultMapBias	0.036	0.004	0.041
defaultPhase	0.000	0.000	0.001
detectAI	0.078	0.003	0.082
fractionPlotDf	0.029	0.003	0.032
gba	0.000	0.000	0.001
genomatrix	0.001	0.000	0.000
genotype2phase	0.023	0.005	0.029
getAlleleCounts	5.445	0.050	5.510
getAlleleQuality	3.590	0.050	3.646
getAreaFromGeneNames	0.652	0.023	0.677
getDefaultMapBiasExpMean	0.024	0.004	0.028
getSnpIdFromLocation	24.056	1.072	25.644
histplot	0	0	0
implodeList-old	0.006	0.000	0.005
import-bam-2	0.009	0.000	0.009
import-bam	32.670	0.241	33.616
import-bcf	1.578	0.015	1.636
inferAlleles	0.011	0.003	0.015
inferAltAllele	0.015	0.003	0.019
inferGenotypes	0.026	0.003	0.030
initialize-ASEset	0.072	0.001	0.073
initialize-DetectedAI	0.082	0.003	0.085
initialize-GlobalAnalysis	0.002	0.004	0.005
initialize-RiskVariant	0.001	0.003	0.004
legendBarplot	0	0	0
locationplot	1.383	0.037	1.420
lva	8.679	0.033	8.712
lva.internal	0.302	0.004	0.306
makeMaskedFasta	1.529	0.017	1.547
mapBiasRef	0.012	0.003	0.016
minCountFilt	0.065	0.004	0.068
minFreqFilt	0.063	0.003	0.065
multiAllelicFilt	0.012	0.003	0.015
phase2genotype	0.022	0.005	0.027
phaseArray2phaseMatrix	0.005	0.003	0.009
phaseMatrix2Array	0.004	0.003	0.009
randomRef	0.019	0.004	0.030
reads	0.000	0.000	0.001
refAllele	0.014	0.004	0.018
regionSummary	0.550	0.005	0.555
scanForHeterozygotes-old	3.901	0.040	3.957

CHECK results for AllelicImbalance on kjohnson1

Summary

Command output

Installation output

Tests output

Example timings