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"	4388
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           32.045  0.235  32.773
getSnpIdFromLocation 24.129  1.162  25.821
lva                   8.172  0.033   8.240
annotation-wrappers   6.772  0.240   7.028
ASEset-glocationplot  5.607  0.068   5.676
getAlleleCounts       5.438  0.056   5.516
* 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 
 22.483   0.872  23.413

Example timings

name	user	system	elapsed
ASEset-barplot	0.223	0.006	0.230
ASEset-class	0.446	0.019	0.465
ASEset-filters	0.055	0.007	0.062
ASEset-gbarplot	0.043	0.006	0.049
ASEset-glocationplot	5.607	0.068	5.676
ASEset-gviztrack	0.644	0.046	0.697
ASEset-scanForHeterozygotes	1.815	0.032	1.848
ASEset.old	0.000	0.000	0.001
ASEset.sim	0.000	0.001	0.000
ASEsetFromBam	0.001	0.003	0.004
DetectedAI-class	0.094	0.004	0.098
DetectedAI-plot	1.256	0.021	1.278
DetectedAI-summary	0.102	0.010	0.111
GRvariants	0.001	0.003	0.005
GlobalAnalysis-class	0.001	0.002	0.003
LinkVariantAlmlof-class	0	0	0
LinkVariantAlmlof-plot	2.090	0.015	2.106
RegionSummary-class	0.000	0.000	0.001
RiskVariant-class	0.000	0.000	0.001
annotation-wrappers	6.772	0.240	7.028
annotationBarplot	0	0	0
barplot-lattice-support	0.114	0.003	0.116
binom.test	0.044	0.003	0.049
chisq.test	0.119	0.003	0.122
cigar-utilities	0.013	0.000	0.014
countAllelesFromBam	0.001	0.003	0.005
coverageMatrixListFromGAL	0.77	0.04	0.81
decorateWithExons	0.001	0.003	0.005
decorateWithGenes	0.001	0.003	0.004
defaultMapBias	0.035	0.006	0.041
defaultPhase	0.000	0.000	0.001
detectAI	0.078	0.003	0.082
fractionPlotDf	0.030	0.003	0.032
gba	0	0	0
genomatrix	0	0	0
genotype2phase	0.024	0.005	0.029
getAlleleCounts	5.438	0.056	5.516
getAlleleQuality	3.563	0.071	3.635
getAreaFromGeneNames	0.688	0.019	0.708
getDefaultMapBiasExpMean	0.023	0.003	0.027
getSnpIdFromLocation	24.129	1.162	25.821
histplot	0.000	0.000	0.001
implodeList-old	0.006	0.000	0.009
import-bam-2	0.008	0.000	0.009
import-bam	32.045	0.235	32.773
import-bcf	1.552	0.022	1.577
inferAlleles	0.011	0.004	0.015
inferAltAllele	0.016	0.004	0.019
inferGenotypes	0.028	0.004	0.032
initialize-ASEset	0.078	0.001	0.080
initialize-DetectedAI	0.083	0.004	0.088
initialize-GlobalAnalysis	0.001	0.004	0.005
initialize-RiskVariant	0.001	0.003	0.004
legendBarplot	0	0	0
locationplot	1.408	0.037	1.461
lva	8.172	0.033	8.240
lva.internal	0.298	0.004	0.301
makeMaskedFasta	1.477	0.022	1.501
mapBiasRef	0.013	0.003	0.016
minCountFilt	0.063	0.004	0.066
minFreqFilt	0.064	0.003	0.067
multiAllelicFilt	0.011	0.003	0.016
phase2genotype	0.022	0.006	0.028
phaseArray2phaseMatrix	0.005	0.003	0.007
phaseMatrix2Array	0.004	0.002	0.006
randomRef	0.019	0.003	0.022
reads	0	0	0
refAllele	0.014	0.004	0.018
regionSummary	0.534	0.004	0.538
scanForHeterozygotes-old	3.963	0.052	4.027

CHECK results for AllelicImbalance on kjohnson1

Summary

Command output

Installation output

Tests output

Example timings