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CHECK report for AllelicImbalance on malbec2

This page was generated on 2019-10-16 12:03:26 -0400 (Wed, 16 Oct 2019).

Package 43/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AllelicImbalance 1.22.0
Jesper R Gadin
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/AllelicImbalance
Branch: RELEASE_3_9
Last Commit: 04692e3
Last Changed Date: 2019-05-02 11:53:45 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: AllelicImbalance
Version: 1.22.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:AllelicImbalance.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings AllelicImbalance_1.22.0.tar.gz
StartedAt: 2019-10-15 23:41:55 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-15 23:49:09 -0400 (Tue, 15 Oct 2019)
EllapsedTime: 434.3 seconds
RetCode: 0
Status:  OK 
CheckDir: AllelicImbalance.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:AllelicImbalance.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings AllelicImbalance_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.22.0’
* 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 or elapsed time > 5s
                       user system elapsed
getSnpIdFromLocation 25.020  1.063  26.153
import-bam           20.917  0.120  21.740
lva                   8.621  0.008   8.637
* 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-3.9-bioc/R/bin/R CMD INSTALL AllelicImbalance
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.9-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 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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, 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: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Loading required package: GenomicAlignments
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:DelayedArray':

    type

The following object is masked from 'package:base':

    strsplit

Loading required package: Rsamtools
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 96 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
> 
> 
> 
> proc.time()
   user  system elapsed 
 16.197   0.575  16.792 

Example timings

AllelicImbalance.Rcheck/AllelicImbalance-Ex.timings

nameusersystemelapsed
ASEset-barplot0.2640.0000.264
ASEset-class1.0990.0201.118
ASEset-filters0.0750.0000.075
ASEset-gbarplot0.0830.0000.083
ASEset-glocationplot4.4540.0804.535
ASEset-gviztrack0.4710.0000.472
ASEset-scanForHeterozygotes1.3370.0001.337
ASEset.old000
ASEset.sim000
ASEsetFromBam0.0010.0000.002
DetectedAI-class0.1360.0000.136
DetectedAI-plot1.3160.0001.315
DetectedAI-summary0.1310.0000.130
GRvariants0.0020.0000.001
GlobalAnalysis-class0.0010.0000.001
LinkVariantAlmlof-class0.0000.0000.001
LinkVariantAlmlof-plot1.6130.0001.613
RegionSummary-class000
RiskVariant-class0.0010.0000.000
annotation-wrappers4.6660.1604.838
annotationBarplot000
barplot-lattice-support0.1540.0000.155
binom.test0.0800.0000.081
chisq.test0.2490.0080.260
cigar-utilities0.0160.0000.016
countAllelesFromBam0.0020.0000.002
coverageMatrixListFromGAL0.7450.0030.748
decorateWithExons0.0020.0000.002
decorateWithGenes0.0010.0000.002
defaultMapBias0.0280.0000.040
defaultPhase000
detectAI0.1490.0000.149
fractionPlotDf0.0460.0000.046
gba000
genomatrix0.0000.0000.001
genotype2phase0.0270.0000.027
getAlleleCounts3.8190.0043.822
getAlleleQuality4.1560.0084.164
getAreaFromGeneNames0.4170.0000.418
getDefaultMapBiasExpMean0.0610.0000.061
getSnpIdFromLocation25.020 1.06326.153
histplot000
implodeList-old0.0050.0000.005
import-bam-20.0050.0000.005
import-bam20.917 0.12021.740
import-bcf0.9110.0200.941
inferAlleles0.0220.0000.022
inferAltAllele0.0250.0000.025
inferGenotypes0.0460.0000.046
initialize-ASEset0.050.000.05
initialize-DetectedAI0.1030.0000.103
initialize-GlobalAnalysis0.0040.0000.004
initialize-RiskVariant0.0010.0000.002
legendBarplot000
locationplot1.4550.0001.455
lva8.6210.0088.637
lva.internal0.3390.0000.340
makeMaskedFasta1.0070.0001.012
mapBiasRef0.0270.0000.030
minCountFilt0.1400.0040.145
minFreqFilt0.1290.0000.129
multiAllelicFilt0.0260.0000.026
phase2genotype0.0430.0000.042
phaseArray2phaseMatrix0.0050.0000.005
phaseMatrix2Array0.0050.0000.004
randomRef0.0290.0000.029
reads0.0010.0000.000
refAllele0.0110.0000.011
regionSummary0.4440.0000.444
scanForHeterozygotes-old3.3790.0003.380