Multiple platform build/check report for BioC 3.19 - CHECK results for AllelicImbalance on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4753
lconway	macOS 12.7.1 Monterey	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4518
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_1.42.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/AllelicImbalance.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-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 Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AllelicImbalance/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AllelicImbalance’ version ‘1.42.0’
* 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               26.151  0.482  26.853
getSnpIdFromLocation     22.800  1.302  24.355
lva                      10.433  0.134  10.667
ASEset-glocationplot      6.042  0.146   6.250
annotation-wrappers       5.213  0.344   5.639
scanForHeterozygotes-old  5.082  0.045   5.155
* 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-3.19-bioc/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/4.4-x86_64/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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 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

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, 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 
 20.444   1.342  21.972

Example timings

name	user	system	elapsed
ASEset-barplot	0.240	0.023	0.266
ASEset-class	0.555	0.015	0.575
ASEset-filters	0.062	0.004	0.069
ASEset-gbarplot	0.039	0.003	0.043
ASEset-glocationplot	6.042	0.146	6.250
ASEset-gviztrack	0.590	0.060	0.658
ASEset-scanForHeterozygotes	2.051	0.045	2.119
ASEset.old	0.000	0.000	0.001
ASEset.sim	0	0	0
ASEsetFromBam	0.001	0.001	0.003
DetectedAI-class	0.091	0.003	0.094
DetectedAI-plot	1.391	0.031	1.435
DetectedAI-summary	0.121	0.009	0.131
GRvariants	0.001	0.003	0.004
GlobalAnalysis-class	0.001	0.003	0.004
LinkVariantAlmlof-class	0	0	0
LinkVariantAlmlof-plot	2.355	0.032	2.408
RegionSummary-class	0	0	0
RiskVariant-class	0	0	0
annotation-wrappers	5.213	0.344	5.639
annotationBarplot	0	0	0
barplot-lattice-support	0.137	0.004	0.143
binom.test	0.057	0.004	0.061
chisq.test	0.159	0.004	0.163
cigar-utilities	0.013	0.001	0.015
countAllelesFromBam	0.002	0.003	0.004
coverageMatrixListFromGAL	0.910	0.014	0.932
decorateWithExons	0.001	0.002	0.003
decorateWithGenes	0.001	0.001	0.002
defaultMapBias	0.041	0.006	0.047
defaultPhase	0.001	0.001	0.001
detectAI	0.101	0.005	0.108
fractionPlotDf	0.235	0.023	0.260
gba	0	0	0
genomatrix	0.000	0.000	0.001
genotype2phase	0.023	0.003	0.027
getAlleleCounts	4.627	0.076	4.744
getAlleleQuality	4.196	0.058	4.298
getAreaFromGeneNames	0.666	0.029	0.704
getDefaultMapBiasExpMean	0.028	0.003	0.031
getSnpIdFromLocation	22.800	1.302	24.355
histplot	0.001	0.000	0.000
implodeList-old	0.004	0.000	0.005
import-bam-2	0.007	0.001	0.008
import-bam	26.151	0.482	26.853
import-bcf	1.347	0.031	1.387
inferAlleles	0.010	0.002	0.012
inferAltAllele	0.014	0.002	0.016
inferGenotypes	0.029	0.002	0.031
initialize-ASEset	0.075	0.001	0.076
initialize-DetectedAI	0.100	0.003	0.105
initialize-GlobalAnalysis	0.002	0.002	0.004
initialize-RiskVariant	0.002	0.003	0.004
legendBarplot	0	0	0
locationplot	1.612	0.029	1.652
lva	10.433	0.134	10.667
lva.internal	0.350	0.006	0.359
makeMaskedFasta	1.198	0.011	1.215
mapBiasRef	0.011	0.002	0.014
minCountFilt	0.070	0.004	0.073
minFreqFilt	0.076	0.004	0.080
multiAllelicFilt	0.010	0.002	0.012
phase2genotype	0.030	0.005	0.035
phaseArray2phaseMatrix	0.004	0.003	0.007
phaseMatrix2Array	0.003	0.002	0.005
randomRef	0.016	0.002	0.018
reads	0	0	0
refAllele	0.015	0.004	0.018
regionSummary	0.597	0.007	0.606
scanForHeterozygotes-old	5.082	0.045	5.155

CHECK results for AllelicImbalance on lconway

Summary

Command output

Installation output

Tests output

Example timings