Multiple platform build/check report for BioC 3.17 - CHECK results for AllelicImbalance on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.1 LTS)	x86_64	R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences"	4547
palomino3	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences"	4308
merida1	macOS 10.14.6 Mojave	x86_64	R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences"	4301
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_1.37.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/AllelicImbalance.Rcheck’
* using R Under development (unstable) (2023-03-16 r83985)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AllelicImbalance/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AllelicImbalance’ version ‘1.37.0’
* 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 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        35.211  1.900  50.437
import-bam                  29.375  0.401  38.746
lva                         21.335  0.055  28.565
scanForHeterozygotes-old    11.647  0.037  15.776
getAlleleCounts              9.418  0.061  12.044
annotation-wrappers          8.477  0.419  11.334
getAlleleQuality             8.185  0.078  10.554
ASEset-glocationplot         7.320  0.155   9.669
LinkVariantAlmlof-plot       4.854  0.027   6.288
ASEset-scanForHeterozygotes  4.113  0.097   5.378
* 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-3.17-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/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 Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences"
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 
 34.469   1.439  47.716

Example timings

name	user	system	elapsed
ASEset-barplot	1.547	0.028	2.006
ASEset-class	0.961	0.035	1.325
ASEset-filters	0.123	0.017	0.183
ASEset-gbarplot	0.084	0.012	0.120
ASEset-glocationplot	7.320	0.155	9.669
ASEset-gviztrack	1.129	0.109	1.550
ASEset-scanForHeterozygotes	4.113	0.097	5.378
ASEset.old	0.000	0.000	0.001
ASEset.sim	0.000	0.000	0.001
ASEsetFromBam	0.002	0.003	0.011
DetectedAI-class	0.219	0.004	0.288
DetectedAI-plot	3.049	0.027	3.949
DetectedAI-summary	0.260	0.012	0.346
GRvariants	0.002	0.004	0.005
GlobalAnalysis-class	0.002	0.003	0.005
LinkVariantAlmlof-class	0	0	0
LinkVariantAlmlof-plot	4.854	0.027	6.288
RegionSummary-class	0.001	0.000	0.000
RiskVariant-class	0.000	0.001	0.000
annotation-wrappers	8.477	0.419	11.334
annotationBarplot	0.000	0.001	0.000
barplot-lattice-support	0.262	0.002	0.460
binom.test	0.103	0.004	0.125
chisq.test	0.306	0.004	0.380
cigar-utilities	0.022	0.000	0.027
countAllelesFromBam	0.002	0.003	0.005
coverageMatrixListFromGAL	1.675	0.005	2.120
decorateWithExons	0.002	0.003	0.007
decorateWithGenes	0.002	0.003	0.004
defaultMapBias	0.074	0.005	0.102
defaultPhase	0.001	0.000	0.003
detectAI	0.212	0.005	0.274
fractionPlotDf	0.070	0.003	0.094
gba	0	0	0
genomatrix	0	0	0
genotype2phase	0.058	0.006	0.064
getAlleleCounts	9.418	0.061	12.044
getAlleleQuality	8.185	0.078	10.554
getAreaFromGeneNames	1.000	0.019	1.361
getDefaultMapBiasExpMean	0.057	0.003	0.082
getSnpIdFromLocation	35.211	1.900	50.437
histplot	0	0	0
implodeList-old	0.011	0.000	0.013
import-bam-2	0.016	0.000	0.022
import-bam	29.375	0.401	38.746
import-bcf	1.480	0.029	1.990
inferAlleles	0.023	0.003	0.039
inferAltAllele	0.036	0.003	0.049
inferGenotypes	0.067	0.003	0.086
initialize-ASEset	0.177	0.002	0.233
initialize-DetectedAI	0.203	0.005	0.275
initialize-GlobalAnalysis	0.002	0.003	0.005
initialize-RiskVariant	0.002	0.003	0.007
legendBarplot	0.000	0.001	0.000
locationplot	3.313	0.040	4.346
lva	21.335	0.055	28.565
lva.internal	0.717	0.005	0.962
makeMaskedFasta	1.355	0.013	1.903
mapBiasRef	0.027	0.003	0.044
minCountFilt	0.151	0.005	0.206
minFreqFilt	0.149	0.004	0.209
multiAllelicFilt	0.024	0.003	0.039
phase2genotype	0.045	0.006	0.071
phaseArray2phaseMatrix	0.008	0.003	0.013
phaseMatrix2Array	0.007	0.004	0.014
randomRef	0.038	0.003	0.059
reads	0	0	0
refAllele	0.028	0.004	0.041
regionSummary	1.289	0.007	1.817
scanForHeterozygotes-old	11.647	0.037	15.776

CHECK results for AllelicImbalance on merida1

Summary

Command output

Installation output

Tests output

Example timings