Multiple platform build/check report for BioC 3.21 - CHECK results for AllelicImbalance on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"	4777
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"	4545
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4576
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4528
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4458
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 lconway

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: 1.45.0

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_1.45.0.tar.gz

StartedAt: 2025-03-20 19:13:58 -0400 (Thu, 20 Mar 2025)

EndedAt: 2025-03-20 19:22:49 -0400 (Thu, 20 Mar 2025)

EllapsedTime: 530.6 seconds

RetCode: 0

Status: OK

CheckDir: AllelicImbalance.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.45.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/AllelicImbalance.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AllelicImbalance/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AllelicImbalance’ version ‘1.45.0’
* 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               26.515  0.418  27.095
getSnpIdFromLocation     23.865  1.451  25.557
lva                       9.774  0.058   9.875
ASEset-glocationplot      6.013  0.087   6.120
getAlleleCounts           5.629  0.068   5.738
annotation-wrappers       5.116  0.299   5.464
scanForHeterozygotes-old  5.126  0.041   5.196
* 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-3.21-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/4.5-x86_64/Resources/library’
* installing *source* package ‘AllelicImbalance’ ...
** this is package ‘AllelicImbalance’ version ‘1.45.0’
** 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 Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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 
 19.795   1.225  21.152

Example timings

AllelicImbalance.Rcheck/AllelicImbalance-Ex.timings

name	user	system	elapsed
ASEset-barplot	0.228	0.009	0.238
ASEset-class	0.448	0.021	0.471
ASEset-filters	0.059	0.009	0.068
ASEset-gbarplot	0.035	0.006	0.041
ASEset-glocationplot	6.013	0.087	6.120
ASEset-gviztrack	0.642	0.056	0.702
ASEset-scanForHeterozygotes	1.831	0.018	1.854
ASEset.old	0	0	0
ASEset.sim	0.000	0.001	0.000
ASEsetFromBam	0.001	0.001	0.002
DetectedAI-class	0.079	0.002	0.081
DetectedAI-plot	1.412	0.021	1.449
DetectedAI-summary	0.136	0.010	0.147
GRvariants	0.001	0.003	0.005
GlobalAnalysis-class	0.001	0.002	0.003
LinkVariantAlmlof-class	0	0	0
LinkVariantAlmlof-plot	2.356	0.019	2.386
RegionSummary-class	0.000	0.000	0.001
RiskVariant-class	0	0	0
annotation-wrappers	5.116	0.299	5.464
annotationBarplot	0	0	0
barplot-lattice-support	0.118	0.003	0.121
binom.test	0.052	0.003	0.055
chisq.test	0.301	0.022	0.325
cigar-utilities	0.012	0.001	0.013
countAllelesFromBam	0.001	0.003	0.003
coverageMatrixListFromGAL	0.862	0.006	0.873
decorateWithExons	0.001	0.002	0.003
decorateWithGenes	0.001	0.002	0.003
defaultMapBias	0.038	0.006	0.045
defaultPhase	0.000	0.000	0.001
detectAI	0.114	0.003	0.118
fractionPlotDf	0.041	0.003	0.045
gba	0	0	0
genomatrix	0.000	0.000	0.001
genotype2phase	0.025	0.004	0.029
getAlleleCounts	5.629	0.068	5.738
getAlleleQuality	4.042	0.025	4.088
getAreaFromGeneNames	0.640	0.028	0.678
getDefaultMapBiasExpMean	0.026	0.002	0.029
getSnpIdFromLocation	23.865	1.451	25.557
histplot	0.000	0.001	0.000
implodeList-old	0.005	0.000	0.006
import-bam-2	0.011	0.001	0.011
import-bam	26.515	0.418	27.095
import-bcf	1.355	0.031	1.394
inferAlleles	0.014	0.003	0.017
inferAltAllele	0.018	0.003	0.021
inferGenotypes	0.031	0.003	0.034
initialize-ASEset	0.085	0.001	0.087
initialize-DetectedAI	0.093	0.002	0.096
initialize-GlobalAnalysis	0.002	0.001	0.003
initialize-RiskVariant	0.002	0.002	0.003
legendBarplot	0	0	0
locationplot	1.555	0.032	1.597
lva	9.774	0.058	9.875
lva.internal	0.388	0.005	0.395
makeMaskedFasta	1.244	0.011	1.261
mapBiasRef	0.013	0.002	0.015
minCountFilt	0.079	0.003	0.081
minFreqFilt	0.085	0.003	0.090
multiAllelicFilt	0.013	0.003	0.015
phase2genotype	0.024	0.005	0.028
phaseArray2phaseMatrix	0.004	0.002	0.006
phaseMatrix2Array	0.003	0.002	0.004
randomRef	0.021	0.002	0.023
reads	0.001	0.000	0.000
refAllele	0.017	0.002	0.019
regionSummary	0.647	0.005	0.658
scanForHeterozygotes-old	5.126	0.041	5.196