Multiple platform build/check report for BioC 3.13 - CHECK results for AllelicImbalance on machv2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AllelicImbalance.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AllelicImbalance_1.30.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/AllelicImbalance.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.30.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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
lva                      196.815  0.414 197.420
LinkVariantAlmlof-plot    40.262  0.092  40.396
getSnpIdFromLocation      23.887  1.421  25.381
import-bam                21.817  0.331  22.198
scanForHeterozygotes-old   8.877  0.040   8.936
annotation-wrappers        5.900  0.256   6.194
getAlleleQuality           5.819  0.020   5.845
ASEset-glocationplot       5.687  0.111   5.802
getAlleleCounts            5.351  0.069   5.423
* 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-3.13-bioc/meat/AllelicImbalance.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL AllelicImbalance
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, 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
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 96 ]
> 
> 
> 
> proc.time()
   user  system elapsed 
 22.225   0.975  23.207

Example timings

name	user	system	elapsed
ASEset-barplot	0.493	0.020	0.513
ASEset-class	0.793	0.045	0.870
ASEset-filters	1.078	0.021	1.103
ASEset-gbarplot	0.081	0.002	0.084
ASEset-glocationplot	5.687	0.111	5.802
ASEset-gviztrack	1.056	0.078	1.135
ASEset-scanForHeterozygotes	2.937	0.017	2.956
ASEset.old	0.000	0.000	0.001
ASEset.sim	0.000	0.001	0.000
ASEsetFromBam	0.002	0.002	0.004
DetectedAI-class	0.306	0.003	0.311
DetectedAI-plot	2.592	0.019	2.615
DetectedAI-summary	0.441	0.012	0.453
GRvariants	0.002	0.002	0.003
GlobalAnalysis-class	0.001	0.002	0.003
LinkVariantAlmlof-class	0	0	0
LinkVariantAlmlof-plot	40.262	0.092	40.396
RegionSummary-class	0.001	0.000	0.000
RiskVariant-class	0.000	0.000	0.001
annotation-wrappers	5.900	0.256	6.194
annotationBarplot	0	0	0
barplot-lattice-support	0.324	0.002	0.328
binom.test	0.198	0.004	0.203
chisq.test	0.457	0.006	0.463
cigar-utilities	0.016	0.000	0.018
countAllelesFromBam	0.001	0.002	0.003
coverageMatrixListFromGAL	1.326	0.010	1.336
decorateWithExons	0.001	0.002	0.003
decorateWithGenes	0.001	0.003	0.004
defaultMapBias	0.059	0.004	0.063
defaultPhase	0.001	0.000	0.001
detectAI	0.368	0.006	0.378
fractionPlotDf	0.089	0.003	0.092
gba	0.001	0.000	0.000
genomatrix	0.000	0.000	0.001
genotype2phase	0.046	0.005	0.050
getAlleleCounts	5.351	0.069	5.423
getAlleleQuality	5.819	0.020	5.845
getAreaFromGeneNames	0.510	0.009	0.520
getDefaultMapBiasExpMean	0.065	0.003	0.068
getSnpIdFromLocation	23.887	1.421	25.381
histplot	0.000	0.001	0.001
implodeList-old	0.006	0.001	0.007
import-bam-2	0.014	0.001	0.015
import-bam	21.817	0.331	22.198
import-bcf	1.209	0.028	1.241
inferAlleles	0.025	0.002	0.028
inferAltAllele	0.055	0.003	0.057
inferGenotypes	0.102	0.004	0.106
initialize-ASEset	0.175	0.002	0.177
initialize-DetectedAI	0.313	0.005	0.318
initialize-GlobalAnalysis	0.006	0.004	0.010
initialize-RiskVariant	0.001	0.002	0.003
legendBarplot	0	0	0
locationplot	2.910	0.024	2.962
lva	196.815	0.414	197.420
lva.internal	1.096	0.010	1.107
makeMaskedFasta	1.106	0.016	1.125
mapBiasRef	0.059	0.005	0.064
minCountFilt	0.167	0.004	0.172
minFreqFilt	0.148	0.004	0.152
multiAllelicFilt	0.023	0.004	0.028
phase2genotype	0.056	0.004	0.061
phaseArray2phaseMatrix	0.030	0.003	0.032
phaseMatrix2Array	0.031	0.002	0.034
randomRef	0.049	0.003	0.053
reads	0.000	0.001	0.001
refAllele	0.035	0.006	0.041
regionSummary	2.110	0.025	2.143
scanForHeterozygotes-old	8.877	0.040	8.936

CHECK results for AllelicImbalance on machv2

Summary

Command output

Installation output

Tests output

Example timings