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This page was generated on 2021-12-03 13:05:38 -0500 (Fri, 03 Dec 2021).

CHECK results for AllelicImbalance on machv2

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raw results

Package 42/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AllelicImbalance 1.32.0  (landing page)
Jesper R Gadin
Snapshot Date: 2021-12-02 01:55:06 -0500 (Thu, 02 Dec 2021)
git_url: https://git.bioconductor.org/packages/AllelicImbalance
git_branch: RELEASE_3_14
git_last_commit: 428ab8c
git_last_commit_date: 2021-10-26 12:10:09 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: AllelicImbalance
Version: 1.32.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AllelicImbalance.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AllelicImbalance_1.32.0.tar.gz
StartedAt: 2021-12-02 11:33:36 -0500 (Thu, 02 Dec 2021)
EndedAt: 2021-12-02 11:46:50 -0500 (Thu, 02 Dec 2021)
EllapsedTime: 793.6 seconds
RetCode: 0
Status:   OK  
CheckDir: AllelicImbalance.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AllelicImbalance.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AllelicImbalance_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/AllelicImbalance.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.32.0’
* 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 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
lva                      146.320  0.402 147.285
getSnpIdFromLocation      30.280  1.441  31.742
LinkVariantAlmlof-plot    29.303  0.113  29.452
import-bam                25.459  0.308  25.886
scanForHeterozygotes-old   9.158  0.032   9.205
annotation-wrappers        7.416  0.266   7.701
ASEset-glocationplot       6.745  0.117   6.869
getAlleleCounts            6.413  0.023   6.442
getAlleleQuality           6.326  0.017   6.351
* 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/Resources/bin/R CMD INSTALL AllelicImbalance
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 4.1.2 (2021-11-01) -- "Bird Hippie"
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

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 
 26.516   1.112  27.633 

Example timings

AllelicImbalance.Rcheck/AllelicImbalance-Ex.timings

nameusersystemelapsed
ASEset-barplot0.4860.0410.526
ASEset-class0.9270.0090.937
ASEset-filters0.1850.0220.206
ASEset-gbarplot0.1420.0160.159
ASEset-glocationplot6.7450.1176.869
ASEset-gviztrack1.1060.0381.144
ASEset-scanForHeterozygotes3.0550.0203.077
ASEset.old000
ASEset.sim0.0000.0000.001
ASEsetFromBam0.0010.0020.004
DetectedAI-class0.3860.0040.391
DetectedAI-plot2.8790.0232.907
DetectedAI-summary0.4520.0150.467
GRvariants0.0010.0020.002
GlobalAnalysis-class0.0010.0020.003
LinkVariantAlmlof-class0.0000.0000.001
LinkVariantAlmlof-plot29.303 0.11329.452
RegionSummary-class0.0000.0000.001
RiskVariant-class000
annotation-wrappers7.4160.2667.701
annotationBarplot000
barplot-lattice-support0.3090.0030.315
binom.test0.1970.0040.201
chisq.test0.3660.0110.377
cigar-utilities0.0140.0010.015
countAllelesFromBam0.0010.0010.003
coverageMatrixListFromGAL1.5280.0151.544
decorateWithExons0.0010.0020.003
decorateWithGenes0.0020.0020.003
defaultMapBias0.0690.0040.072
defaultPhase0.0010.0010.001
detectAI0.4340.0040.439
fractionPlotDf0.1050.0040.109
gba0.0010.0010.000
genomatrix000
genotype2phase0.0610.0040.066
getAlleleCounts6.4130.0236.442
getAlleleQuality6.3260.0176.351
getAreaFromGeneNames0.6180.0060.624
getDefaultMapBiasExpMean0.0880.0050.092
getSnpIdFromLocation30.280 1.44131.742
histplot000
implodeList-old0.0090.0000.010
import-bam-20.0190.0010.021
import-bam25.459 0.30825.886
import-bcf1.2640.0261.291
inferAlleles0.0350.0030.038
inferAltAllele0.0570.0040.061
inferGenotypes0.0840.0030.087
initialize-ASEset0.2020.0010.204
initialize-DetectedAI0.3780.0030.382
initialize-GlobalAnalysis0.0060.0040.010
initialize-RiskVariant0.0010.0020.004
legendBarplot0.0000.0010.001
locationplot3.4730.0403.517
lva146.320 0.402147.285
lva.internal1.1640.0121.199
makeMaskedFasta1.1310.0221.158
mapBiasRef0.0420.0030.044
minCountFilt0.1760.0050.181
minFreqFilt0.1760.0060.183
multiAllelicFilt0.0300.0060.036
phase2genotype0.0740.0070.082
phaseArray2phaseMatrix0.0430.0040.047
phaseMatrix2Array0.0360.0040.041
randomRef0.0580.0050.063
reads0.0000.0000.001
refAllele0.0370.0050.043
regionSummary2.0320.0292.069
scanForHeterozygotes-old9.1580.0329.205