Build/check report for BioC 3.17 - CHECK results for AllelicImbalance on kunpeng1

Hostname	OS	Arch (*)	R version	Installed pkgs
kunpeng1	Linux (Ubuntu 22.04.1 LTS)	aarch64	R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"	4164
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:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:AllelicImbalance.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings AllelicImbalance_1.37.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/AllelicImbalance.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* 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 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘AllelicImbalance/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AllelicImbalance’ version ‘1.37.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
getSnpIdFromLocation     29.016  1.435  30.549
import-bam               29.247  0.204  29.503
lva                      13.049  0.016  13.067
scanForHeterozygotes-old  7.030  0.004   7.034
getAlleleCounts           5.791  0.000   5.803
annotation-wrappers       5.505  0.195   6.153
ASEset-glocationplot      5.618  0.020   5.643
getAlleleQuality          5.139  0.001   5.141
* 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-3.17-bioc/meat/AllelicImbalance.Rcheck/00check.log’
for details.

Installation output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL AllelicImbalance
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
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 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 
 22.790   0.788  23.567

Example timings

name	user	system	elapsed
ASEset-barplot	0.260	0.008	0.274
ASEset-class	0.555	0.084	0.642
ASEset-filters	0.071	0.008	0.079
ASEset-gbarplot	0.051	0.004	0.055
ASEset-glocationplot	5.618	0.020	5.643
ASEset-gviztrack	0.662	0.068	0.731
ASEset-scanForHeterozygotes	2.572	0.032	2.606
ASEset.old	0.001	0.000	0.000
ASEset.sim	0	0	0
ASEsetFromBam	0.001	0.000	0.002
DetectedAI-class	0.133	0.000	0.132
DetectedAI-plot	1.863	0.004	1.868
DetectedAI-summary	0.159	0.004	0.164
GRvariants	0.002	0.000	0.002
GlobalAnalysis-class	0.001	0.000	0.002
LinkVariantAlmlof-class	0	0	0
LinkVariantAlmlof-plot	3.119	0.016	3.139
RegionSummary-class	0	0	0
RiskVariant-class	0	0	0
annotation-wrappers	5.505	0.195	6.153
annotationBarplot	0	0	0
barplot-lattice-support	0.159	0.004	0.166
binom.test	0.066	0.000	0.067
chisq.test	0.189	0.000	0.189
cigar-utilities	0.016	0.000	0.016
countAllelesFromBam	0.001	0.000	0.001
coverageMatrixListFromGAL	1.013	0.000	1.014
decorateWithExons	0.001	0.000	0.001
decorateWithGenes	0.000	0.001	0.001
defaultMapBias	0.044	0.002	0.047
defaultPhase	0.001	0.000	0.001
detectAI	0.125	0.004	0.129
fractionPlotDf	0.040	0.004	0.043
gba	0	0	0
genomatrix	0.001	0.000	0.000
genotype2phase	0.032	0.004	0.035
getAlleleCounts	5.791	0.000	5.803
getAlleleQuality	5.139	0.001	5.141
getAreaFromGeneNames	0.443	0.000	0.443
getDefaultMapBiasExpMean	0.033	0.000	0.034
getSnpIdFromLocation	29.016	1.435	30.549
histplot	0	0	0
implodeList-old	0.003	0.004	0.007
import-bam-2	0.011	0.000	0.011
import-bam	29.247	0.204	29.503
import-bcf	1.427	0.004	1.435
inferAlleles	0.011	0.004	0.014
inferAltAllele	0.021	0.000	0.021
inferGenotypes	0.042	0.000	0.041
initialize-ASEset	0.108	0.000	0.109
initialize-DetectedAI	0.124	0.000	0.123
initialize-GlobalAnalysis	0.001	0.000	0.002
initialize-RiskVariant	0.001	0.000	0.002
legendBarplot	0.000	0.000	0.001
locationplot	1.939	0.000	1.940
lva	13.049	0.016	13.067
lva.internal	0.48	0.00	0.48
makeMaskedFasta	1.35	0.00	1.35
mapBiasRef	0.016	0.000	0.016
minCountFilt	0.093	0.000	0.093
minFreqFilt	0.097	0.000	0.097
multiAllelicFilt	0.012	0.003	0.015
phase2genotype	0.032	0.000	0.032
phaseArray2phaseMatrix	0.006	0.000	0.006
phaseMatrix2Array	0.006	0.000	0.005
randomRef	0.024	0.000	0.025
reads	0.000	0.000	0.001
refAllele	0.018	0.000	0.018
regionSummary	0.791	0.000	0.791
scanForHeterozygotes-old	7.030	0.004	7.034

CHECK results for AllelicImbalance on kunpeng1

Summary

Command output

Installation output

Tests output

Example timings