Build/check report for BioC 3.18 - CHECK results for AllelicImbalance on kunpeng1

Hostname	OS	Arch (*)	R version	Installed pkgs
kunpeng1	Linux (Ubuntu 22.04.1 LTS)	aarch64	4.3.0 (2023-04-21) -- "Already Tomorrow"	4219
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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###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:AllelicImbalance.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings AllelicImbalance_1.39.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/AllelicImbalance.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘AllelicImbalance/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AllelicImbalance’ version ‘1.39.0’
* 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
getSnpIdFromLocation     31.060  2.689  33.752
import-bam               29.639  0.380  30.062
lva                      11.883  0.096  11.980
scanForHeterozygotes-old  7.108  0.024   7.132
getAlleleCounts           6.739  0.280   7.019
ASEset-glocationplot      6.768  0.216   6.984
annotation-wrappers       5.530  0.226   5.765
* 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 ...
  ‘AllelicImbalance-vignette.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/AllelicImbalance.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL AllelicImbalance
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* installing to library ‘/home/biocbuild/R/R-4.3.0/site-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 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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 ═══════════════════════════════════════════════════════════════
• empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 96 ]
> 
> 
> 
> proc.time()
   user  system elapsed 
 23.609   1.205  24.800

Example timings

name	user	system	elapsed
ASEset-barplot	0.238	0.003	0.242
ASEset-class	0.556	0.027	0.584
ASEset-filters	0.062	0.021	0.082
ASEset-gbarplot	0.054	0.000	0.054
ASEset-glocationplot	6.768	0.216	6.984
ASEset-gviztrack	0.677	0.071	0.749
ASEset-scanForHeterozygotes	2.481	0.040	2.521
ASEset.old	0	0	0
ASEset.sim	0	0	0
ASEsetFromBam	0.000	0.002	0.002
DetectedAI-class	0.123	0.004	0.127
DetectedAI-plot	1.822	0.055	1.878
DetectedAI-summary	0.156	0.004	0.160
GRvariants	0.002	0.000	0.002
GlobalAnalysis-class	0.002	0.000	0.002
LinkVariantAlmlof-class	0	0	0
LinkVariantAlmlof-plot	2.814	0.059	2.874
RegionSummary-class	0	0	0
RiskVariant-class	0	0	0
annotation-wrappers	5.530	0.226	5.765
annotationBarplot	0.001	0.000	0.000
barplot-lattice-support	0.160	0.000	0.159
binom.test	0.064	0.004	0.067
chisq.test	0.182	0.000	0.182
cigar-utilities	0.011	0.004	0.014
countAllelesFromBam	0.002	0.000	0.002
coverageMatrixListFromGAL	1.001	0.020	1.021
decorateWithExons	0.001	0.000	0.002
decorateWithGenes	0.001	0.000	0.001
defaultMapBias	0.046	0.000	0.047
defaultPhase	0.001	0.000	0.001
detectAI	0.121	0.004	0.125
fractionPlotDf	0.093	0.011	0.104
gba	0	0	0
genomatrix	0	0	0
genotype2phase	0.036	0.000	0.036
getAlleleCounts	6.739	0.280	7.019
getAlleleQuality	4.745	0.012	4.757
getAreaFromGeneNames	0.548	0.016	0.565
getDefaultMapBiasExpMean	0.033	0.000	0.033
getSnpIdFromLocation	31.060	2.689	33.752
histplot	0	0	0
implodeList-old	0.008	0.000	0.008
import-bam-2	0.012	0.000	0.013
import-bam	29.639	0.380	30.062
import-bcf	1.427	0.012	1.441
inferAlleles	0.014	0.000	0.014
inferAltAllele	0.02	0.00	0.02
inferGenotypes	0.04	0.00	0.04
initialize-ASEset	0.106	0.000	0.106
initialize-DetectedAI	0.122	0.000	0.122
initialize-GlobalAnalysis	0.000	0.002	0.001
initialize-RiskVariant	0.000	0.002	0.001
legendBarplot	0	0	0
locationplot	1.936	0.040	1.976
lva	11.883	0.096	11.980
lva.internal	0.446	0.004	0.449
makeMaskedFasta	1.361	0.024	1.385
mapBiasRef	0.013	0.004	0.016
minCountFilt	0.09	0.00	0.09
minFreqFilt	0.085	0.004	0.088
multiAllelicFilt	0.015	0.000	0.014
phase2genotype	0.029	0.000	0.028
phaseArray2phaseMatrix	0.006	0.000	0.005
phaseMatrix2Array	0.005	0.000	0.004
randomRef	0.020	0.004	0.024
reads	0	0	0
refAllele	0.019	0.000	0.018
regionSummary	0.752	0.004	0.756
scanForHeterozygotes-old	7.108	0.024	7.132

CHECK results for AllelicImbalance on kunpeng1

Summary

Command output

Installation output

Tests output

Example timings