Package: AllelicImbalance

Version: 1.24.0

Command: /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_1.24.0.tar.gz

StartedAt: 2020-04-15 00:18:59 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 00:27:38 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 519.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: AllelicImbalance.Rcheck

Warnings: 1

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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_1.24.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.24.0’
* 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 ... 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 ... WARNING
Documented arguments not in \usage in documentation object 'RiskVariant-class':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 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 or elapsed time > 5s
                           user system elapsed
getSnpIdFromLocation     24.183  1.904  26.405
import-bam               20.570  0.437  21.282
lva                      15.294  0.045  15.485
annotation-wrappers       6.424  0.263   6.782
scanForHeterozygotes-old  6.329  0.020   6.402
ASEset-glocationplot      5.600  0.158   5.819
getAlleleCounts           5.304  0.016   5.352
getAlleleQuality          5.213  0.025   5.277
* 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 WARNING
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/AllelicImbalance.Rcheck/00check.log’
for details.

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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/3.6/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)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
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")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply, rowsum

Loading required package: GenomicAlignments
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: Rsamtools
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 96 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
> 
> 
> 
> proc.time()
   user  system elapsed 
 21.700   1.025  22.873 

name	user	system	elapsed
ASEset-barplot	0.685	0.010	0.699
ASEset-class	1.494	0.077	1.586
ASEset-filters	0.184	0.002	0.188
ASEset-gbarplot	0.113	0.002	0.116
ASEset-glocationplot	5.600	0.158	5.819
ASEset-gviztrack	0.705	0.016	0.726
ASEset-scanForHeterozygotes	2.737	0.020	2.811
ASEset.old	0	0	0
ASEset.sim	0	0	0
ASEsetFromBam	0.001	0.002	0.003
DetectedAI-class	0.356	0.002	0.362
DetectedAI-plot	2.582	0.015	2.624
DetectedAI-summary	0.347	0.008	0.358
GRvariants	0.002	0.003	0.004
GlobalAnalysis-class	0.002	0.002	0.004
LinkVariantAlmlof-class	0	0	0
LinkVariantAlmlof-plot	3.011	0.021	3.091
RegionSummary-class	0	0	0
RiskVariant-class	0.000	0.001	0.000
annotation-wrappers	6.424	0.263	6.782
annotationBarplot	0.000	0.001	0.000
barplot-lattice-support	0.337	0.005	0.345
binom.test	0.268	0.010	0.280
chisq.test	0.526	0.029	0.558
cigar-utilities	0.019	0.001	0.019
countAllelesFromBam	0.002	0.002	0.005
coverageMatrixListFromGAL	1.007	0.002	1.017
decorateWithExons	0.002	0.002	0.004
decorateWithGenes	0.002	0.001	0.003
defaultMapBias	0.051	0.004	0.054
defaultPhase	0.001	0.000	0.002
detectAI	0.372	0.005	0.383
fractionPlotDf	0.089	0.003	0.091
gba	0	0	0
genomatrix	0	0	0
genotype2phase	0.037	0.003	0.039
getAlleleCounts	5.304	0.016	5.352
getAlleleQuality	5.213	0.025	5.277
getAreaFromGeneNames	0.455	0.009	0.468
getDefaultMapBiasExpMean	0.098	0.003	0.102
getSnpIdFromLocation	24.183	1.904	26.405
histplot	0	0	0
implodeList-old	0.008	0.000	0.008
import-bam-2	0.011	0.000	0.012
import-bam	20.570	0.437	21.282
import-bcf	1.015	0.028	1.056
inferAlleles	0.067	0.002	0.069
inferAltAllele	0.093	0.003	0.098
inferGenotypes	0.163	0.003	0.167
initialize-ASEset	0.113	0.001	0.115
initialize-DetectedAI	0.301	0.003	0.308
initialize-GlobalAnalysis	0.006	0.002	0.008
initialize-RiskVariant	0.002	0.003	0.004
legendBarplot	0.001	0.000	0.000
locationplot	3.555	0.028	3.613
lva	15.294	0.045	15.485
lva.internal	0.619	0.003	0.626
makeMaskedFasta	1.000	0.005	1.010
mapBiasRef	0.042	0.002	0.044
minCountFilt	0.317	0.002	0.321
minFreqFilt	0.304	0.002	0.307
multiAllelicFilt	0.065	0.002	0.068
phase2genotype	0.066	0.004	0.072
phaseArray2phaseMatrix	0.005	0.001	0.007
phaseMatrix2Array	0.005	0.001	0.007
randomRef	0.067	0.002	0.071
reads	0.000	0.000	0.001
refAllele	0.019	0.002	0.020
regionSummary	1.064	0.019	1.095
scanForHeterozygotes-old	6.329	0.020	6.402