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This page was generated on 2021-10-23 14:05:53 -0400 (Sat, 23 Oct 2021).

CHECK results for AllelicImbalance on nebbiolo2

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raw results

Package 42/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AllelicImbalance 1.31.0  (landing page)
Jesper R Gadin
Snapshot Date: 2021-10-22 14:50:11 -0400 (Fri, 22 Oct 2021)
git_url: https://git.bioconductor.org/packages/AllelicImbalance
git_branch: master
git_last_commit: b838792
git_last_commit_date: 2021-05-19 12:00:58 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: AllelicImbalance
Version: 1.31.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:AllelicImbalance.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings AllelicImbalance_1.31.0.tar.gz
StartedAt: 2021-10-22 19:03:52 -0400 (Fri, 22 Oct 2021)
EndedAt: 2021-10-22 19:12:13 -0400 (Fri, 22 Oct 2021)
EllapsedTime: 501.7 seconds
RetCode: 0
Status:   OK  
CheckDir: AllelicImbalance.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:AllelicImbalance.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings AllelicImbalance_1.31.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/AllelicImbalance.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.31.0’
* 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 LazyData ... 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
lva                    79.084  0.220  79.305
import-bam             27.860  0.224  28.095
getSnpIdFromLocation   21.508  1.963  23.474
LinkVariantAlmlof-plot 16.197  0.180  16.378
* 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: OK


Installation output

AllelicImbalance.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL AllelicImbalance
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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 4.1.1 (2021-08-10) -- "Kick Things"
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

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, 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 
 18.621   0.790  19.397 

Example timings

AllelicImbalance.Rcheck/AllelicImbalance-Ex.timings

nameusersystemelapsed
ASEset-barplot0.2790.0120.291
ASEset-class0.4500.0840.535
ASEset-filters0.0930.0090.101
ASEset-gbarplot0.1070.0040.111
ASEset-glocationplot4.8680.0924.959
ASEset-gviztrack0.6130.0710.685
ASEset-scanForHeterozygotes1.6230.0241.647
ASEset.old0.0000.0000.001
ASEset.sim000
ASEsetFromBam0.0010.0000.002
DetectedAI-class0.2100.0000.209
DetectedAI-plot1.4760.0241.500
DetectedAI-summary0.2510.0000.252
GRvariants0.0010.0000.002
GlobalAnalysis-class0.0010.0000.001
LinkVariantAlmlof-class000
LinkVariantAlmlof-plot16.197 0.18016.378
RegionSummary-class000
RiskVariant-class000
annotation-wrappers3.7410.1763.918
annotationBarplot000
barplot-lattice-support0.1570.0030.162
binom.test0.1010.0000.101
chisq.test0.2240.0040.227
cigar-utilities0.0110.0000.010
countAllelesFromBam0.0020.0000.001
coverageMatrixListFromGAL0.8710.0240.894
decorateWithExons0.0020.0000.001
decorateWithGenes0.0010.0000.000
defaultMapBias0.0440.0000.044
defaultPhase0.0010.0000.001
detectAI0.1890.0040.193
fractionPlotDf0.0510.0000.050
gba000
genomatrix0.0000.0000.001
genotype2phase0.0260.0000.026
getAlleleCounts3.8030.0323.835
getAlleleQuality3.6270.0523.680
getAreaFromGeneNames0.3290.0000.329
getDefaultMapBiasExpMean0.040.000.04
getSnpIdFromLocation21.508 1.96323.474
histplot000
implodeList-old0.0040.0000.004
import-bam-20.0110.0000.012
import-bam27.860 0.22428.095
import-bcf1.4720.0121.484
inferAlleles0.0180.0000.018
inferAltAllele0.0320.0000.031
inferGenotypes0.0590.0000.059
initialize-ASEset0.1100.0280.139
initialize-DetectedAI0.2120.0000.212
initialize-GlobalAnalysis0.0040.0000.004
initialize-RiskVariant0.0010.0000.002
legendBarplot000
locationplot1.6980.0041.702
lva79.084 0.22079.305
lva.internal0.6650.0000.666
makeMaskedFasta1.3830.0281.411
mapBiasRef0.0340.0040.037
minCountFilt0.1000.0000.099
minFreqFilt0.0940.0000.094
multiAllelicFilt0.0180.0000.017
phase2genotype0.0350.0040.038
phaseArray2phaseMatrix0.0210.0000.020
phaseMatrix2Array0.0210.0000.021
randomRef0.0310.0000.031
reads000
refAllele0.0210.0000.021
regionSummary1.1830.0001.183
scanForHeterozygotes-old4.9800.0004.979