Multiple platform build/check report for BioC 3.20 - CHECK results for AllelicImbalance on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4746
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4489
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4517
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4469
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4387
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*

CHECK results for AllelicImbalance on kjohnson1

To the developers/maintainers of the AllelicImbalance package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AllelicImbalance.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: AllelicImbalance

Version: 1.44.0

Command: /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_1.44.0.tar.gz

StartedAt: 2025-01-14 10:56:49 -0500 (Tue, 14 Jan 2025)

EndedAt: 2025-01-14 11:05:47 -0500 (Tue, 14 Jan 2025)

EllapsedTime: 538.3 seconds

RetCode: 0

Status: OK

CheckDir: AllelicImbalance.Rcheck

Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /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_1.44.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/AllelicImbalance.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* 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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AllelicImbalance/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AllelicImbalance’ version ‘1.44.0’
* 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 code 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               32.614  0.242  33.541
getSnpIdFromLocation     22.580  1.282  23.983
lva                       8.235  0.045   8.328
ASEset-glocationplot      6.861  0.082   6.946
annotation-wrappers       5.169  0.245   5.441
scanForHeterozygotes-old  4.998  0.054   5.090
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.20-bioc/meat/AllelicImbalance.Rcheck/00check.log’
for details.

Installation output

AllelicImbalance.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL AllelicImbalance
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-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

AllelicImbalance.Rcheck/tests/test-all.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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, saveRDS, setdiff, 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 
 23.041   1.143  24.374

Example timings

AllelicImbalance.Rcheck/AllelicImbalance-Ex.timings

name	user	system	elapsed
ASEset-barplot	0.215	0.014	0.229
ASEset-class	0.487	0.033	0.521
ASEset-filters	0.052	0.004	0.056
ASEset-gbarplot	0.039	0.003	0.042
ASEset-glocationplot	6.861	0.082	6.946
ASEset-gviztrack	0.611	0.043	0.654
ASEset-scanForHeterozygotes	1.860	0.054	1.916
ASEset.old	0	0	0
ASEset.sim	0	0	0
ASEsetFromBam	0.001	0.003	0.005
DetectedAI-class	0.090	0.004	0.094
DetectedAI-plot	1.280	0.021	1.303
DetectedAI-summary	0.109	0.009	0.119
GRvariants	0.001	0.003	0.004
GlobalAnalysis-class	0.001	0.003	0.004
LinkVariantAlmlof-class	0	0	0
LinkVariantAlmlof-plot	2.052	0.015	2.068
RegionSummary-class	0.000	0.000	0.001
RiskVariant-class	0	0	0
annotation-wrappers	5.169	0.245	5.441
annotationBarplot	0	0	0
barplot-lattice-support	0.113	0.002	0.116
binom.test	0.047	0.003	0.051
chisq.test	0.129	0.004	0.132
cigar-utilities	0.015	0.001	0.015
countAllelesFromBam	0.002	0.003	0.004
coverageMatrixListFromGAL	0.726	0.003	0.730
decorateWithExons	0.001	0.004	0.005
decorateWithGenes	0.001	0.003	0.003
defaultMapBias	0.036	0.006	0.044
defaultPhase	0.001	0.001	0.001
detectAI	0.083	0.004	0.086
fractionPlotDf	0.031	0.003	0.034
gba	0	0	0
genomatrix	0	0	0
genotype2phase	0.026	0.006	0.031
getAlleleCounts	4.299	0.091	4.395
getAlleleQuality	3.622	0.028	3.649
getAreaFromGeneNames	0.747	0.025	0.774
getDefaultMapBiasExpMean	0.026	0.003	0.030
getSnpIdFromLocation	22.580	1.282	23.983
histplot	0.000	0.001	0.000
implodeList-old	0.005	0.000	0.006
import-bam-2	0.008	0.000	0.009
import-bam	32.614	0.242	33.541
import-bcf	1.570	0.020	1.592
inferAlleles	0.012	0.005	0.017
inferAltAllele	0.016	0.003	0.020
inferGenotypes	0.028	0.003	0.030
initialize-ASEset	0.074	0.002	0.076
initialize-DetectedAI	0.083	0.004	0.088
initialize-GlobalAnalysis	0.002	0.003	0.004
initialize-RiskVariant	0.001	0.002	0.004
legendBarplot	0.000	0.000	0.001
locationplot	1.456	0.037	1.502
lva	8.235	0.045	8.328
lva.internal	0.333	0.006	0.342
makeMaskedFasta	1.606	0.021	1.651
mapBiasRef	0.014	0.003	0.017
minCountFilt	0.075	0.005	0.082
minFreqFilt	0.070	0.005	0.075
multiAllelicFilt	0.014	0.005	0.018
phase2genotype	0.027	0.007	0.035
phaseArray2phaseMatrix	0.004	0.004	0.008
phaseMatrix2Array	0.004	0.003	0.007
randomRef	0.023	0.003	0.028
reads	0	0	0
refAllele	0.015	0.004	0.019
regionSummary	0.631	0.006	0.648
scanForHeterozygotes-old	4.998	0.054	5.090