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CHECK report for AllelicImbalance on merida1

This page was generated on 2021-01-22 11:57:41 -0500 (Fri, 22 Jan 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: 2021-01-21 14:42:12 -0500 (Thu, 21 Jan 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)
malbec1 Linux (Ubuntu 18.04.5 LTS) / x86_64  OK  ERROR  skipped 
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] ERROR 

Summary

Package: AllelicImbalance
Version: 1.28.0
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_1.28.0.tar.gz
StartedAt: 2021-01-21 23:00:19 -0500 (Thu, 21 Jan 2021)
EndedAt: 2021-01-21 23:10:29 -0500 (Thu, 21 Jan 2021)
EllapsedTime: 609.2 seconds
RetCode: 0
Status:  OK 
CheckDir: AllelicImbalance.Rcheck
Warnings: 0

Command output

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###
### Running 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_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/AllelicImbalance.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.28.0’
* 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 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
getSnpIdFromLocation     24.418  1.508  26.087
import-bam               23.439  0.363  23.860
lva                      16.132  0.049  16.203
scanForHeterozygotes-old  7.942  0.043   7.995
annotation-wrappers       6.647  0.271   6.948
getAlleleCounts           6.046  0.060   6.114
getAlleleQuality          5.448  0.026   5.481
ASEset-glocationplot      5.359  0.086   5.462
* 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:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL AllelicImbalance
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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

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-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 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 
 23.860   0.980  26.221 

Example timings

AllelicImbalance.Rcheck/AllelicImbalance-Ex.timings

nameusersystemelapsed
ASEset-barplot0.3780.0070.386
ASEset-class0.6750.0560.732
ASEset-filters0.0810.0110.091
ASEset-gbarplot0.0750.0120.087
ASEset-glocationplot5.3590.0865.462
ASEset-gviztrack0.9370.0781.018
ASEset-scanForHeterozygotes2.5410.0212.573
ASEset.old000
ASEset.sim000
ASEsetFromBam0.0010.0020.003
DetectedAI-class0.1440.0030.147
DetectedAI-plot1.8090.0161.832
DetectedAI-summary0.1840.0100.194
GRvariants0.0020.0020.005
GlobalAnalysis-class0.0020.0040.005
LinkVariantAlmlof-class0.0010.0010.001
LinkVariantAlmlof-plot3.5360.0193.561
RegionSummary-class0.0010.0000.000
RiskVariant-class0.0010.0000.000
annotation-wrappers6.6470.2716.948
annotationBarplot0.0000.0010.000
barplot-lattice-support0.1690.0020.172
binom.test0.0790.0030.083
chisq.test0.2400.0040.244
cigar-utilities0.0170.0010.017
countAllelesFromBam0.0020.0030.004
coverageMatrixListFromGAL1.1260.0121.140
decorateWithExons0.0020.0030.004
decorateWithGenes0.0020.0030.004
defaultMapBias0.0590.0050.064
defaultPhase0.0010.0000.002
detectAI0.1510.0030.155
fractionPlotDf0.0420.0020.044
gba0.0000.0000.001
genomatrix0.0000.0000.001
genotype2phase0.0370.0040.041
getAlleleCounts6.0460.0606.114
getAlleleQuality5.4480.0265.481
getAreaFromGeneNames0.4350.0090.445
getDefaultMapBiasExpMean0.0390.0030.043
getSnpIdFromLocation24.418 1.50826.087
histplot000
implodeList-old0.0070.0010.008
import-bam-20.0150.0010.016
import-bam23.439 0.36323.860
import-bcf1.1290.0271.158
inferAlleles0.0240.0020.026
inferAltAllele0.0330.0030.036
inferGenotypes0.0670.0040.070
initialize-ASEset0.1110.0010.112
initialize-DetectedAI0.1580.0040.162
initialize-GlobalAnalysis0.0070.0020.010
initialize-RiskVariant0.0010.0030.005
legendBarplot0.0010.0010.001
locationplot2.5730.0252.601
lva16.132 0.04916.203
lva.internal0.5570.0090.570
makeMaskedFasta1.0830.0151.103
mapBiasRef0.0320.0040.037
minCountFilt0.1270.0050.133
minFreqFilt0.1270.0040.132
multiAllelicFilt0.0210.0040.025
phase2genotype0.0400.0040.044
phaseArray2phaseMatrix0.0120.0030.014
phaseMatrix2Array0.0110.0040.015
randomRef0.0340.0030.037
reads0.0000.0010.000
refAllele0.0280.0040.033
regionSummary1.0050.0111.019
scanForHeterozygotes-old7.9420.0437.995