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"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4467
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: 2024-12-20 11:00:12 -0500 (Fri, 20 Dec 2024)

EndedAt: 2024-12-20 11:09:07 -0500 (Fri, 20 Dec 2024)

EllapsedTime: 534.2 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_1.44.0.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           32.640  0.247  33.583
getSnpIdFromLocation 22.438  1.203  23.721
lva                   8.068  0.040   8.146
ASEset-glocationplot  6.792  0.077   6.877
annotation-wrappers   5.150  0.232   5.419
* 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 
 22.932   1.081  24.130

Example timings

AllelicImbalance.Rcheck/AllelicImbalance-Ex.timings

name	user	system	elapsed
ASEset-barplot	0.215	0.009	0.224
ASEset-class	0.480	0.026	0.506
ASEset-filters	0.050	0.004	0.053
ASEset-gbarplot	0.038	0.003	0.042
ASEset-glocationplot	6.792	0.077	6.877
ASEset-gviztrack	0.619	0.042	0.662
ASEset-scanForHeterozygotes	1.813	0.034	1.847
ASEset.old	0	0	0
ASEset.sim	0	0	0
ASEsetFromBam	0.001	0.003	0.005
DetectedAI-class	0.091	0.004	0.094
DetectedAI-plot	1.270	0.024	1.295
DetectedAI-summary	0.110	0.009	0.120
GRvariants	0.002	0.004	0.009
GlobalAnalysis-class	0.002	0.003	0.005
LinkVariantAlmlof-class	0	0	0
LinkVariantAlmlof-plot	2.062	0.014	2.077
RegionSummary-class	0	0	0
RiskVariant-class	0	0	0
annotation-wrappers	5.150	0.232	5.419
annotationBarplot	0	0	0
barplot-lattice-support	0.115	0.002	0.118
binom.test	0.049	0.004	0.053
chisq.test	0.124	0.004	0.128
cigar-utilities	0.012	0.001	0.013
countAllelesFromBam	0.002	0.003	0.005
coverageMatrixListFromGAL	0.707	0.002	0.710
decorateWithExons	0.001	0.002	0.005
decorateWithGenes	0.001	0.003	0.004
defaultMapBias	0.034	0.005	0.041
defaultPhase	0.001	0.000	0.001
detectAI	0.088	0.005	0.093
fractionPlotDf	0.033	0.004	0.037
gba	0	0	0
genomatrix	0	0	0
genotype2phase	0.026	0.007	0.032
getAlleleCounts	4.248	0.098	4.346
getAlleleQuality	3.680	0.024	3.704
getAreaFromGeneNames	0.751	0.023	0.775
getDefaultMapBiasExpMean	0.025	0.003	0.027
getSnpIdFromLocation	22.438	1.203	23.721
histplot	0.000	0.001	0.001
implodeList-old	0.006	0.001	0.005
import-bam-2	0.009	0.001	0.010
import-bam	32.640	0.247	33.583
import-bcf	1.560	0.017	1.588
inferAlleles	0.011	0.003	0.014
inferAltAllele	0.015	0.003	0.018
inferGenotypes	0.026	0.003	0.029
initialize-ASEset	0.070	0.002	0.071
initialize-DetectedAI	0.080	0.004	0.083
initialize-GlobalAnalysis	0.002	0.003	0.004
initialize-RiskVariant	0.001	0.003	0.003
legendBarplot	0.000	0.001	0.000
locationplot	1.404	0.046	1.469
lva	8.068	0.040	8.146
lva.internal	0.316	0.006	0.322
makeMaskedFasta	1.532	0.025	1.559
mapBiasRef	0.010	0.004	0.014
minCountFilt	0.059	0.004	0.064
minFreqFilt	0.064	0.004	0.068
multiAllelicFilt	0.010	0.003	0.013
phase2genotype	0.026	0.006	0.033
phaseArray2phaseMatrix	0.003	0.001	0.005
phaseMatrix2Array	0.002	0.001	0.005
randomRef	0.014	0.002	0.016
reads	0	0	0
refAllele	0.009	0.004	0.013
regionSummary	0.398	0.005	0.409
scanForHeterozygotes-old	4.844	0.041	4.960