Multiple platform build/check report for BioC 3.18 - CHECK results for AllelicImbalance on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes"	4692
palomino4	Windows Server 2022 Datacenter	x64	4.3.2 (2023-10-31 ucrt) -- "Eye Holes"	4445
lconway	macOS 12.7.1 Monterey	x86_64	4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"	4466
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/meat/AllelicImbalance.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    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 ‘1.40.0’
* 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               26.294  0.538  27.078
getSnpIdFromLocation     23.836  1.426  25.474
lva                      10.993  0.136  11.237
scanForHeterozygotes-old  5.483  0.057   5.585
annotation-wrappers       5.204  0.328   5.595
getAlleleCounts           5.044  0.106   5.187
getAlleleQuality          5.102  0.044   5.177
ASEset-glocationplot      4.977  0.107   5.133
* 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/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-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 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-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 
 20.947   1.215  22.336

Example timings

name	user	system	elapsed
ASEset-barplot	0.201	0.006	0.208
ASEset-class	0.490	0.025	0.518
ASEset-filters	0.065	0.010	0.076
ASEset-gbarplot	0.046	0.007	0.053
ASEset-glocationplot	4.977	0.107	5.133
ASEset-gviztrack	0.592	0.056	0.653
ASEset-scanForHeterozygotes	2.051	0.046	2.111
ASEset.old	0	0	0
ASEset.sim	0.000	0.000	0.001
ASEsetFromBam	0.001	0.002	0.003
DetectedAI-class	0.112	0.003	0.116
DetectedAI-plot	1.442	0.029	1.481
DetectedAI-summary	0.143	0.009	0.154
GRvariants	0.001	0.002	0.003
GlobalAnalysis-class	0.002	0.003	0.003
LinkVariantAlmlof-class	0.000	0.000	0.001
LinkVariantAlmlof-plot	2.465	0.027	2.514
RegionSummary-class	0	0	0
RiskVariant-class	0.000	0.001	0.000
annotation-wrappers	5.204	0.328	5.595
annotationBarplot	0.000	0.000	0.001
barplot-lattice-support	0.115	0.003	0.120
binom.test	0.056	0.003	0.059
chisq.test	0.157	0.004	0.162
cigar-utilities	0.011	0.001	0.011
countAllelesFromBam	0.002	0.003	0.003
coverageMatrixListFromGAL	0.807	0.005	0.816
decorateWithExons	0.002	0.003	0.004
decorateWithGenes	0.002	0.003	0.004
defaultMapBias	0.037	0.007	0.047
defaultPhase	0.001	0.000	0.001
detectAI	0.113	0.002	0.116
fractionPlotDf	0.038	0.002	0.040
gba	0.000	0.001	0.000
genomatrix	0	0	0
genotype2phase	0.031	0.004	0.036
getAlleleCounts	5.044	0.106	5.187
getAlleleQuality	5.102	0.044	5.177
getAreaFromGeneNames	0.628	0.028	0.662
getDefaultMapBiasExpMean	0.031	0.003	0.034
getSnpIdFromLocation	23.836	1.426	25.474
histplot	0	0	0
implodeList-old	0.007	0.001	0.008
import-bam-2	0.008	0.001	0.009
import-bam	26.294	0.538	27.078
import-bcf	1.286	0.032	1.330
inferAlleles	0.014	0.003	0.016
inferAltAllele	0.018	0.003	0.022
inferGenotypes	0.037	0.003	0.041
initialize-ASEset	0.093	0.002	0.096
initialize-DetectedAI	0.108	0.005	0.114
initialize-GlobalAnalysis	0.002	0.002	0.004
initialize-RiskVariant	0.002	0.003	0.004
legendBarplot	0.000	0.000	0.001
locationplot	1.656	0.037	1.710
lva	10.993	0.136	11.237
lva.internal	0.406	0.009	0.419
makeMaskedFasta	1.177	0.017	1.205
mapBiasRef	0.012	0.002	0.015
minCountFilt	0.077	0.004	0.082
minFreqFilt	0.075	0.004	0.079
multiAllelicFilt	0.014	0.004	0.018
phase2genotype	0.023	0.004	0.028
phaseArray2phaseMatrix	0.005	0.003	0.008
phaseMatrix2Array	0.004	0.003	0.008
randomRef	0.022	0.002	0.024
reads	0.000	0.001	0.000
refAllele	0.016	0.003	0.019
regionSummary	0.668	0.010	0.684
scanForHeterozygotes-old	5.483	0.057	5.585

CHECK results for AllelicImbalance on lconway

Summary

Command output

Installation output

Tests output

Example timings