Mac ARM64 build report for BioC 3.17 - CHECK results for AllelicImbalance on kjohnson2

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson2	macOS 12.6.1 Monterey	arm64	4.3.1 (2023-06-16) -- "Beagle Scouts"	4347
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_1.38.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/AllelicImbalance.Rcheck’
* using R version 4.3.1 (2023-06-16)
* 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 Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AllelicImbalance/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AllelicImbalance’ version ‘1.38.0’
* 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
getSnpIdFromLocation     29.210  1.588  46.609
import-bam               22.624  0.399  33.656
lva                      11.250  0.118  17.325
annotation-wrappers       6.289  0.284  10.103
scanForHeterozygotes-old  6.318  0.058   9.736
getAlleleCounts           5.231  0.061   7.802
ASEset-glocationplot      4.849  0.080   6.476
getAlleleQuality          4.519  0.044   6.931
* 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-3.17-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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 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 
 20.530   0.985  32.390

Example timings

name	user	system	elapsed
ASEset-barplot	0.243	0.022	0.269
ASEset-class	0.508	0.054	0.574
ASEset-filters	0.061	0.008	0.071
ASEset-gbarplot	0.048	0.007	0.057
ASEset-glocationplot	4.849	0.080	6.476
ASEset-gviztrack	0.692	0.052	1.154
ASEset-scanForHeterozygotes	2.263	0.058	3.601
ASEset.old	0	0	0
ASEset.sim	0	0	0
ASEsetFromBam	0.001	0.002	0.004
DetectedAI-class	0.152	0.008	0.244
DetectedAI-plot	1.512	0.026	2.470
DetectedAI-summary	0.137	0.012	0.255
GRvariants	0.001	0.002	0.003
GlobalAnalysis-class	0.001	0.002	0.005
LinkVariantAlmlof-class	0	0	0
LinkVariantAlmlof-plot	2.620	0.034	4.196
RegionSummary-class	0	0	0
RiskVariant-class	0.001	0.000	0.000
annotation-wrappers	6.289	0.284	10.103
annotationBarplot	0	0	0
barplot-lattice-support	0.140	0.004	0.203
binom.test	0.060	0.003	0.092
chisq.test	0.156	0.003	0.229
cigar-utilities	0.013	0.001	0.021
countAllelesFromBam	0.001	0.002	0.006
coverageMatrixListFromGAL	0.940	0.009	1.446
decorateWithExons	0.002	0.002	0.005
decorateWithGenes	0.001	0.001	0.009
defaultMapBias	0.041	0.004	0.068
defaultPhase	0.000	0.001	0.004
detectAI	0.109	0.004	0.174
fractionPlotDf	0.039	0.003	0.066
gba	0.000	0.000	0.001
genomatrix	0	0	0
genotype2phase	0.029	0.004	0.051
getAlleleCounts	5.231	0.061	7.802
getAlleleQuality	4.519	0.044	6.931
getAreaFromGeneNames	0.558	0.021	0.864
getDefaultMapBiasExpMean	0.029	0.002	0.049
getSnpIdFromLocation	29.210	1.588	46.609
histplot	0.000	0.000	0.001
implodeList-old	0.007	0.001	0.016
import-bam-2	0.012	0.002	0.023
import-bam	22.624	0.399	33.656
import-bcf	1.112	0.019	1.741
inferAlleles	0.013	0.002	0.025
inferAltAllele	0.018	0.002	0.031
inferGenotypes	0.032	0.002	0.055
initialize-ASEset	0.095	0.002	0.151
initialize-DetectedAI	0.106	0.003	0.168
initialize-GlobalAnalysis	0.001	0.002	0.007
initialize-RiskVariant	0.001	0.002	0.004
legendBarplot	0	0	0
locationplot	1.813	0.076	2.873
lva	11.250	0.118	17.325
lva.internal	0.383	0.006	0.580
makeMaskedFasta	1.026	0.011	1.544
mapBiasRef	0.013	0.002	0.024
minCountFilt	0.084	0.004	0.139
minFreqFilt	0.077	0.003	0.125
multiAllelicFilt	0.013	0.003	0.023
phase2genotype	0.026	0.005	0.047
phaseArray2phaseMatrix	0.005	0.003	0.010
phaseMatrix2Array	0.004	0.003	0.009
randomRef	0.023	0.002	0.037
reads	0.000	0.000	0.001
refAllele	0.016	0.003	0.029
regionSummary	0.715	0.009	1.103
scanForHeterozygotes-old	6.318	0.058	9.736

CHECK results for AllelicImbalance on kjohnson2

Summary

Command output

Installation output

Tests output

Example timings