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CHECK report for AllelicImbalance on malbec1

This page was generated on 2019-04-16 11:50:14 -0400 (Tue, 16 Apr 2019).

Package 39/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AllelicImbalance 1.20.0
Jesper R Gadin
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/AllelicImbalance
Branch: RELEASE_3_8
Last Commit: 4cd3a78
Last Changed Date: 2018-10-30 11:41:52 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: AllelicImbalance
Version: 1.20.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:AllelicImbalance.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings AllelicImbalance_1.20.0.tar.gz
StartedAt: 2019-04-15 22:08:56 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 22:15:51 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 415.1 seconds
RetCode: 0
Status:  OK 
CheckDir: AllelicImbalance.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:AllelicImbalance.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings AllelicImbalance_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.20.0’
* 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 22.056  1.116  23.219
import-bam           20.876  0.140  21.132
lva                   8.808  0.028   8.846
annotation-wrappers   5.688  0.144   5.866
* 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-3.8-bioc/R/bin/R CMD INSTALL AllelicImbalance
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘AllelicImbalance’ ...
** 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
* DONE (AllelicImbalance)

Tests output

AllelicImbalance.Rcheck/tests/test-all.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, 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

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 FAILED: 0
> 
> 
> 
> proc.time()
   user  system elapsed 
 16.100   0.424  16.557 

Example timings

AllelicImbalance.Rcheck/AllelicImbalance-Ex.timings

nameusersystemelapsed
ASEset-barplot0.4040.0040.411
ASEset-class0.6960.0360.734
ASEset-filters0.1240.0040.128
ASEset-gbarplot0.0880.0000.087
ASEset-glocationplot4.0280.0044.032
ASEset-gviztrack0.7240.0000.727
ASEset-scanForHeterozygotes2.3720.0042.379
ASEset.old000
ASEset.sim000
ASEsetFromBam0.0000.0000.002
DetectedAI-class0.2360.0040.246
DetectedAI-plot2.2160.0002.214
DetectedAI-summary0.2480.0000.250
GRvariants0.0000.0000.002
GlobalAnalysis-class0.0040.0000.002
LinkVariantAlmlof-class000
LinkVariantAlmlof-plot2.2560.0002.259
RegionSummary-class000
RiskVariant-class0.0000.0000.001
annotation-wrappers5.6880.1445.866
annotationBarplot000
barplot-lattice-support0.1680.0000.166
binom.test0.0880.0000.089
chisq.test0.1960.0000.195
cigar-utilities0.0080.0040.009
countAllelesFromBam0.0000.0000.002
coverageMatrixListFromGAL1.1080.0001.113
decorateWithExons0.0000.0040.003
decorateWithGenes0.0000.0000.002
defaultMapBias0.040.000.06
defaultPhase0.0000.0000.001
detectAI0.1360.0040.140
fractionPlotDf0.0400.0000.039
gba000
genomatrix000
genotype2phase0.0280.0000.025
getAlleleCounts3.4200.0043.426
getAlleleQuality3.5720.0003.577
getAreaFromGeneNames0.4440.0040.450
getDefaultMapBiasExpMean0.0720.0000.071
getSnpIdFromLocation22.056 1.11623.219
histplot000
implodeList-old0.0080.0000.005
import-bam-20.0080.0000.006
import-bam20.876 0.14021.132
import-bcf1.0280.0081.041
inferAlleles0.0480.0000.046
inferAltAllele0.0560.0000.056
inferGenotypes0.1000.0040.101
initialize-ASEset0.1040.0000.106
initialize-DetectedAI0.2200.0000.221
initialize-GlobalAnalysis0.0040.0000.006
initialize-RiskVariant0.0000.0000.002
legendBarplot000
locationplot2.3720.0482.421
lva8.8080.0288.846
lva.internal0.4320.0000.433
makeMaskedFasta1.0440.0041.049
mapBiasRef0.0240.0000.027
minCountFilt0.1240.0000.124
minFreqFilt0.1640.0000.167
multiAllelicFilt0.0440.0000.045
phase2genotype0.0600.0000.061
phaseArray2phaseMatrix0.0040.0040.009
phaseMatrix2Array0.0080.0000.008
randomRef0.0520.0000.054
reads000
refAllele0.0240.0000.020
regionSummary0.7800.0000.782
scanForHeterozygotes-old4.4120.0044.419