Multiple platform build/check report for BioC 3.16 - CHECK results for AllelicImbalance on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.5 LTS)	x86_64	4.2.3 (2023-03-15) -- "Shortstop Beagle"	4502
palomino4	Windows Server 2022 Datacenter	x64	4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"	4282
lconway	macOS 12.5.1 Monterey	x86_64	4.2.3 (2023-03-15) -- "Shortstop Beagle"	4310
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*

##############################################################################
##############################################################################
###
### 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_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/AllelicImbalance.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AllelicImbalance/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AllelicImbalance’ version ‘1.36.0’
* 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 ... OK
* 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           23.319  0.270  23.640
getSnpIdFromLocation 20.056  1.041  21.158
lva                   8.523  0.032   8.569
* 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: OK

Installation output

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 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 ═══════════════════════════════════════════════════════════════
• empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 96 ]
> 
> 
> 
> proc.time()
   user  system elapsed 
 17.277   0.824  18.141

Example timings

name	user	system	elapsed
ASEset-barplot	0.192	0.017	0.209
ASEset-class	0.345	0.042	0.387
ASEset-filters	0.046	0.008	0.054
ASEset-gbarplot	0.032	0.005	0.036
ASEset-glocationplot	3.991	0.057	4.057
ASEset-gviztrack	0.454	0.044	0.498
ASEset-scanForHeterozygotes	1.494	0.037	1.532
ASEset.old	0.001	0.000	0.000
ASEset.sim	0	0	0
ASEsetFromBam	0.001	0.002	0.003
DetectedAI-class	0.084	0.003	0.087
DetectedAI-plot	1.073	0.017	1.092
DetectedAI-summary	0.132	0.009	0.142
GRvariants	0.001	0.002	0.002
GlobalAnalysis-class	0.001	0.002	0.003
LinkVariantAlmlof-class	0	0	0
LinkVariantAlmlof-plot	1.919	0.012	1.934
RegionSummary-class	0	0	0
RiskVariant-class	0	0	0
annotation-wrappers	3.986	0.200	4.208
annotationBarplot	0	0	0
barplot-lattice-support	0.114	0.002	0.118
binom.test	0.043	0.002	0.044
chisq.test	0.120	0.003	0.124
cigar-utilities	0.011	0.001	0.011
countAllelesFromBam	0.001	0.002	0.002
coverageMatrixListFromGAL	0.699	0.003	0.704
decorateWithExons	0.001	0.002	0.003
decorateWithGenes	0.001	0.003	0.003
defaultMapBias	0.067	0.004	0.072
defaultPhase	0.001	0.000	0.001
detectAI	0.082	0.002	0.084
fractionPlotDf	0.024	0.002	0.025
gba	0.001	0.000	0.000
genomatrix	0.000	0.001	0.000
genotype2phase	0.020	0.003	0.022
getAlleleCounts	3.700	0.086	3.798
getAlleleQuality	3.103	0.015	3.122
getAreaFromGeneNames	0.352	0.007	0.360
getDefaultMapBiasExpMean	0.023	0.002	0.024
getSnpIdFromLocation	20.056	1.041	21.158
histplot	0	0	0
implodeList-old	0.006	0.001	0.006
import-bam-2	0.009	0.001	0.009
import-bam	23.319	0.270	23.640
import-bcf	1.135	0.019	1.156
inferAlleles	0.009	0.002	0.011
inferAltAllele	0.012	0.002	0.014
inferGenotypes	0.021	0.002	0.023
initialize-ASEset	0.067	0.001	0.067
initialize-DetectedAI	0.085	0.003	0.088
initialize-GlobalAnalysis	0.002	0.002	0.003
initialize-RiskVariant	0.001	0.002	0.002
legendBarplot	0	0	0
locationplot	1.249	0.023	1.276
lva	8.523	0.032	8.569
lva.internal	0.327	0.004	0.331
makeMaskedFasta	1.154	0.041	1.200
mapBiasRef	0.012	0.002	0.014
minCountFilt	0.071	0.003	0.076
minFreqFilt	0.054	0.002	0.057
multiAllelicFilt	0.011	0.003	0.014
phase2genotype	0.022	0.004	0.026
phaseArray2phaseMatrix	0.004	0.002	0.005
phaseMatrix2Array	0.005	0.003	0.007
randomRef	0.016	0.003	0.018
reads	0	0	0
refAllele	0.011	0.002	0.013
regionSummary	0.471	0.003	0.474
scanForHeterozygotes-old	4.257	0.025	4.290

CHECK results for AllelicImbalance on lconway

Summary

Command output

Installation output

Tests output

Example timings