Back to Multiple platform build/check report for BioC 3.12
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for AllelicImbalance on merida1

This page was generated on 2021-04-17 12:10:12 -0400 (Sat, 17 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: 2021-04-16 14:50:12 -0400 (Fri, 16 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: /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: 2021-04-16 22:41:52 -0400 (Fri, 16 Apr 2021)
EndedAt: 2021-04-16 22:51:03 -0400 (Fri, 16 Apr 2021)
EllapsedTime: 550.8 seconds
RetCode: 0
Status:   OK  
CheckDir: AllelicImbalance.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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 4.0.5 (2021-03-31)
* 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     22.887  1.154  24.140
import-bam               22.168  0.343  22.557
lva                      14.504  0.041  14.563
scanForHeterozygotes-old  6.719  0.024   6.748
annotation-wrappers       5.678  0.243   5.929
getAlleleCounts           5.738  0.083   5.882
getAlleleQuality          5.655  0.021   5.681
* 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

##############################################################################
##############################################################################
###
### 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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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 
 21.852   0.913  24.067 

Example timings

AllelicImbalance.Rcheck/AllelicImbalance-Ex.timings

nameusersystemelapsed
ASEset-barplot0.3100.0070.318
ASEset-class0.5580.0530.614
ASEset-filters0.0690.0020.071
ASEset-gbarplot0.0480.0020.050
ASEset-glocationplot4.6720.0754.764
ASEset-gviztrack0.7970.0620.862
ASEset-scanForHeterozygotes2.4770.0232.510
ASEset.old0.0000.0010.001
ASEset.sim000
ASEsetFromBam0.0030.0040.006
DetectedAI-class0.1490.0030.153
DetectedAI-plot1.7900.0181.813
DetectedAI-summary0.1860.0130.198
GRvariants0.0020.0030.005
GlobalAnalysis-class0.0010.0020.003
LinkVariantAlmlof-class0.0000.0010.001
LinkVariantAlmlof-plot3.1630.0133.179
RegionSummary-class0.0000.0000.001
RiskVariant-class000
annotation-wrappers5.6780.2435.929
annotationBarplot0.0000.0010.000
barplot-lattice-support0.1840.0020.187
binom.test0.0980.0020.101
chisq.test0.2360.0030.239
cigar-utilities0.0180.0010.019
countAllelesFromBam0.0020.0040.005
coverageMatrixListFromGAL1.1940.0171.211
decorateWithExons0.0020.0030.005
decorateWithGenes0.0010.0010.003
defaultMapBias0.0490.0040.054
defaultPhase0.0010.0010.001
detectAI0.1520.0040.157
fractionPlotDf0.0490.0020.050
gba0.0000.0000.001
genomatrix000
genotype2phase0.0380.0040.042
getAlleleCounts5.7380.0835.882
getAlleleQuality5.6550.0215.681
getAreaFromGeneNames0.3790.0050.385
getDefaultMapBiasExpMean0.0360.0020.038
getSnpIdFromLocation22.887 1.15424.140
histplot000
implodeList-old0.0080.0000.009
import-bam-20.0150.0010.016
import-bam22.168 0.34322.557
import-bcf1.1140.0201.135
inferAlleles0.0220.0030.025
inferAltAllele0.0290.0030.032
inferGenotypes0.0590.0040.063
initialize-ASEset0.0980.0010.099
initialize-DetectedAI0.1160.0020.117
initialize-GlobalAnalysis0.0040.0020.006
initialize-RiskVariant0.0020.0020.003
legendBarplot000
locationplot1.9480.0341.986
lva14.504 0.04114.563
lva.internal0.5560.0050.562
makeMaskedFasta0.9790.0170.997
mapBiasRef0.0200.0020.023
minCountFilt0.0810.0020.084
minFreqFilt0.0820.0020.084
multiAllelicFilt0.0160.0030.018
phase2genotype0.0280.0030.033
phaseArray2phaseMatrix0.0140.0040.018
phaseMatrix2Array0.0090.0030.011
randomRef0.0310.0030.034
reads0.0010.0000.000
refAllele0.0250.0030.029
regionSummary0.8480.0090.859
scanForHeterozygotes-old6.7190.0246.748