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CHECK report for AllelicImbalance on malbec1

This page was generated on 2021-04-14 12:08:35 -0400 (Wed, 14 Apr 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  (landing page)
Jesper R Gadin
Snapshot Date: 2021-04-13 14:50:13 -0400 (Tue, 13 Apr 2021)
URL: https://git.bioconductor.org/packages/AllelicImbalance
Branch: RELEASE_3_12
Last Commit: ac5d13c
Last Changed Date: 2020-10-27 10:53:07 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
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: 2021-04-13 22:56:36 -0400 (Tue, 13 Apr 2021)
EndedAt: 2021-04-13 23:05:37 -0400 (Tue, 13 Apr 2021)
EllapsedTime: 540.5 seconds
RetCode: 0
Status:   OK  
CheckDir: AllelicImbalance.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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 4.0.5 (2021-03-31)
* 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               24.624  0.160  25.036
getSnpIdFromLocation     22.008  1.016  23.287
lva                      13.104  0.004  13.126
scanForHeterozygotes-old  6.644  0.004   6.658
getAlleleCounts           6.032  0.008   6.049
annotation-wrappers       5.144  0.144   6.096
* 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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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 
 21.824   0.548  23.779 

Example timings

AllelicImbalance.Rcheck/AllelicImbalance-Ex.timings

nameusersystemelapsed
ASEset-barplot0.2480.0040.255
ASEset-class0.7040.0640.768
ASEset-filters0.0880.0000.091
ASEset-gbarplot0.0480.0000.048
ASEset-glocationplot4.4240.0364.464
ASEset-gviztrack0.6240.0320.659
ASEset-scanForHeterozygotes2.5120.0002.516
ASEset.old000
ASEset.sim000
ASEsetFromBam0.0000.0000.001
DetectedAI-class0.1360.0000.138
DetectedAI-plot1.3640.0001.366
DetectedAI-summary0.1360.0000.133
GRvariants0.0000.0000.001
GlobalAnalysis-class0.0040.0000.001
LinkVariantAlmlof-class000
LinkVariantAlmlof-plot3.0120.0043.022
RegionSummary-class000
RiskVariant-class000
annotation-wrappers5.1440.1446.096
annotationBarplot000
barplot-lattice-support0.2080.0040.212
binom.test0.0640.0000.065
chisq.test0.1560.0000.155
cigar-utilities0.0120.0000.012
countAllelesFromBam0.0000.0000.002
coverageMatrixListFromGAL1.1240.0041.127
decorateWithExons0.0000.0000.002
decorateWithGenes0.0000.0000.002
defaultMapBias0.0560.0040.097
defaultPhase0.0040.0000.001
detectAI0.1760.0000.178
fractionPlotDf0.0600.0000.062
gba0.0040.0000.001
genomatrix0.0000.0000.001
genotype2phase0.0280.0040.034
getAlleleCounts6.0320.0086.049
getAlleleQuality4.9400.0044.958
getAreaFromGeneNames0.3720.0000.374
getDefaultMapBiasExpMean0.0360.0000.035
getSnpIdFromLocation22.008 1.01623.287
histplot000
implodeList-old0.0120.0000.009
import-bam-20.0120.0000.013
import-bam24.624 0.16025.036
import-bcf1.2120.0041.221
inferAlleles0.0160.0000.013
inferAltAllele0.020.000.02
inferGenotypes0.0400.0000.037
initialize-ASEset0.0760.0000.075
initialize-DetectedAI0.1120.0000.113
initialize-GlobalAnalysis0.0040.0000.004
initialize-RiskVariant0.0040.0000.001
legendBarplot000
locationplot2.0280.0002.043
lva13.104 0.00413.126
lva.internal0.3520.0000.352
makeMaskedFasta0.9920.0000.993
mapBiasRef0.0240.0040.029
minCountFilt0.1160.0040.120
minFreqFilt0.1200.0000.121
multiAllelicFilt0.0240.0000.024
phase2genotype0.0440.0000.044
phaseArray2phaseMatrix0.0120.0000.013
phaseMatrix2Array0.0120.0000.012
randomRef0.0360.0000.036
reads000
refAllele0.0240.0000.026
regionSummary1.0120.0041.020
scanForHeterozygotes-old6.6440.0046.658