Multiple platform build/check report for BioC 3.18 - CHECK results for AllelicImbalance on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.3.3 (2024-02-29) -- "Angel Food Cake"	4676
palomino4	Windows Server 2022 Datacenter	x64	4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"	4414
merida1	macOS 12.7.1 Monterey	x86_64	4.3.3 (2024-02-29) -- "Angel Food Cake"	4437
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 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* 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 ‘1.40.0’
* 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
getSnpIdFromLocation     34.200  2.097  36.716
import-bam               29.728  0.394  30.758
lva                      20.653  0.100  21.679
scanForHeterozygotes-old 11.658  0.052  11.862
annotation-wrappers      10.143  0.612  11.248
getAlleleCounts           9.359  0.059   9.572
getAlleleQuality          8.173  0.050   8.418
ASEset-glocationplot      7.475  0.142   7.692
* 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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 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 
 34.888   1.874  37.008

Example timings

name	user	system	elapsed
ASEset-barplot	0.373	0.009	0.386
ASEset-class	0.985	0.058	1.054
ASEset-filters	0.123	0.021	0.145
ASEset-gbarplot	0.089	0.016	0.105
ASEset-glocationplot	7.475	0.142	7.692
ASEset-gviztrack	1.141	0.137	1.284
ASEset-scanForHeterozygotes	4.021	0.063	4.092
ASEset.old	0.000	0.001	0.001
ASEset.sim	0	0	0
ASEsetFromBam	0.002	0.004	0.007
DetectedAI-class	0.221	0.006	0.232
DetectedAI-plot	3.032	0.038	3.179
DetectedAI-summary	0.262	0.022	0.288
GRvariants	0.002	0.004	0.006
GlobalAnalysis-class	0.002	0.004	0.006
LinkVariantAlmlof-class	0.000	0.000	0.001
LinkVariantAlmlof-plot	4.521	0.023	4.597
RegionSummary-class	0.000	0.000	0.001
RiskVariant-class	0.000	0.001	0.001
annotation-wrappers	10.143	0.612	11.248
annotationBarplot	0	0	0
barplot-lattice-support	0.260	0.003	0.266
binom.test	0.113	0.006	0.120
chisq.test	0.306	0.007	0.315
cigar-utilities	0.021	0.001	0.022
countAllelesFromBam	0.002	0.005	0.007
coverageMatrixListFromGAL	1.761	0.071	1.859
decorateWithExons	0.002	0.005	0.007
decorateWithGenes	0.002	0.005	0.007
defaultMapBias	0.068	0.007	0.077
defaultPhase	0.001	0.001	0.002
detectAI	0.207	0.005	0.215
fractionPlotDf	0.070	0.005	0.077
gba	0	0	0
genomatrix	0	0	0
genotype2phase	0.061	0.009	0.071
getAlleleCounts	9.359	0.059	9.572
getAlleleQuality	8.173	0.050	8.418
getAreaFromGeneNames	1.180	0.044	1.247
getDefaultMapBiasExpMean	0.056	0.005	0.063
getSnpIdFromLocation	34.200	2.097	36.716
histplot	0.000	0.001	0.000
implodeList-old	0.011	0.001	0.011
import-bam-2	0.018	0.002	0.020
import-bam	29.728	0.394	30.758
import-bcf	1.512	0.021	1.588
inferAlleles	0.024	0.005	0.030
inferAltAllele	0.035	0.005	0.042
inferGenotypes	0.070	0.005	0.080
initialize-ASEset	0.184	0.002	0.192
initialize-DetectedAI	0.208	0.006	0.227
initialize-GlobalAnalysis	0.002	0.005	0.010
initialize-RiskVariant	0.002	0.005	0.008
legendBarplot	0.000	0.000	0.001
locationplot	3.372	0.044	3.563
lva	20.653	0.100	21.679
lva.internal	0.738	0.009	0.775
makeMaskedFasta	1.297	0.011	1.371
mapBiasRef	0.025	0.006	0.031
minCountFilt	0.151	0.006	0.158
minFreqFilt	0.150	0.006	0.156
multiAllelicFilt	0.024	0.008	0.032
phase2genotype	0.049	0.010	0.059
phaseArray2phaseMatrix	0.007	0.005	0.013
phaseMatrix2Array	0.007	0.005	0.012
randomRef	0.041	0.005	0.050
reads	0.000	0.001	0.002
refAllele	0.030	0.006	0.039
regionSummary	1.311	0.014	1.386
scanForHeterozygotes-old	11.658	0.052	11.862

CHECK results for AllelicImbalance on merida1

Summary

Command output

Installation output

Tests output

Example timings