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CHECK report for AllelicImbalance on nebbiolo1

This page was generated on 2021-02-22 12:33:03 -0500 (Mon, 22 Feb 2021).

To the developers/maintainers of the AllelicImbalance package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 44/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AllelicImbalance 1.28.0
Jesper R Gadin
Snapshot Date: 2021-02-21 14:52:07 -0500 (Sun, 21 Feb 2021)
URL: https://git.bioconductor.org/packages/AllelicImbalance
Branch: RELEASE_3_12
Last Commit: ac5d13c
Last Changed Date: 2020-10-27 10:53:07 -0500 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: AllelicImbalance
Version: 1.28.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:AllelicImbalance.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings AllelicImbalance_1.28.0.tar.gz
StartedAt: 2021-02-21 20:11:24 -0500 (Sun, 21 Feb 2021)
EndedAt: 2021-02-21 20:18:57 -0500 (Sun, 21 Feb 2021)
EllapsedTime: 453.5 seconds
RetCode: 0
Status:   OK  
CheckDir: AllelicImbalance.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:AllelicImbalance.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings AllelicImbalance_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/AllelicImbalance.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (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 ‘1.28.0’
* 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 ... 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 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
import-bam           26.275  0.252  26.540
getSnpIdFromLocation 18.139  1.668  19.809
lva                   9.169  0.056   9.225
* 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: OK


Installation output

AllelicImbalance.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL AllelicImbalance
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-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

AllelicImbalance.Rcheck/tests/test-all.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-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
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 object is masked from 'package:base':

    expand.grid

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:base':

    strsplit

Loading required package: Rsamtools
══ Skipped tests ═══════════════════════════════════════════════════════════════
● empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 96 ]
> 
> 
> 
> proc.time()
   user  system elapsed 
 17.302   1.409  21.592 

Example timings

AllelicImbalance.Rcheck/AllelicImbalance-Ex.timings

nameusersystemelapsed
ASEset-barplot0.2250.0040.228
ASEset-class0.3860.0600.446
ASEset-filters0.0520.0000.052
ASEset-gbarplot0.0420.0000.042
ASEset-glocationplot4.5500.0644.613
ASEset-gviztrack0.5590.0520.612
ASEset-scanForHeterozygotes1.6710.0161.688
ASEset.old0.0010.0000.000
ASEset.sim000
ASEsetFromBam0.0000.0020.002
DetectedAI-class0.1090.0000.109
DetectedAI-plot1.2890.0041.293
DetectedAI-summary0.1250.0080.133
GRvariants0.0010.0000.002
GlobalAnalysis-class0.0020.0000.002
LinkVariantAlmlof-class0.0010.0000.000
LinkVariantAlmlof-plot2.2670.0282.295
RegionSummary-class0.0010.0000.000
RiskVariant-class000
annotation-wrappers3.5600.3083.868
annotationBarplot0.0010.0000.001
barplot-lattice-support0.1060.0000.106
binom.test0.0480.0000.048
chisq.test0.1260.0000.125
cigar-utilities0.0100.0000.011
countAllelesFromBam0.0020.0000.002
coverageMatrixListFromGAL0.7150.0040.719
decorateWithExons0.0000.0020.002
decorateWithGenes0.0000.0020.002
defaultMapBias0.0290.0040.032
defaultPhase0.0020.0000.001
detectAI0.0830.0000.083
fractionPlotDf0.0320.0000.032
gba0.0000.0000.001
genomatrix0.0000.0000.001
genotype2phase0.0220.0020.024
getAlleleCounts4.0310.0044.036
getAlleleQuality3.6580.0203.677
getAreaFromGeneNames0.3200.0000.321
getDefaultMapBiasExpMean0.0310.0040.036
getSnpIdFromLocation18.139 1.66819.809
histplot000
implodeList-old0.0050.0000.005
import-bam-20.0080.0000.008
import-bam26.275 0.25226.540
import-bcf1.3130.0161.329
inferAlleles0.0150.0000.014
inferAltAllele0.0210.0000.022
inferGenotypes0.0350.0000.034
initialize-ASEset0.0690.0000.069
initialize-DetectedAI0.0900.0000.091
initialize-GlobalAnalysis0.0040.0000.004
initialize-RiskVariant0.0020.0000.002
legendBarplot000
locationplot1.3900.0001.391
lva9.1690.0569.225
lva.internal0.3480.0040.352
makeMaskedFasta1.2180.0001.218
mapBiasRef0.0180.0000.019
minCountFilt0.0670.0000.067
minFreqFilt0.0620.0000.061
multiAllelicFilt0.0050.0080.013
phase2genotype0.0230.0000.024
phaseArray2phaseMatrix0.0070.0000.008
phaseMatrix2Array0.0070.0000.006
randomRef0.020.000.02
reads000
refAllele0.0110.0040.015
regionSummary0.5460.0000.546
scanForHeterozygotes-old4.6750.0004.676