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CHECK report for AllelicImbalance on malbec1

This page was generated on 2018-04-12 13:11:34 -0400 (Thu, 12 Apr 2018).

Package 35/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AllelicImbalance 1.16.0
Jesper R Gadin
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/AllelicImbalance
Branch: RELEASE_3_6
Last Commit: 85f652a
Last Changed Date: 2017-10-30 12:40:08 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: AllelicImbalance
Version: 1.16.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.16.0.tar.gz
StartedAt: 2018-04-11 21:22:45 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 21:29:02 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 376.3 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-3.6-bioc/R/bin/R CMD check --no-vignettes --timings AllelicImbalance_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/AllelicImbalance.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.16.0’
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
getSnpIdFromLocation 18.372  0.968  24.944
import-bam           14.236  0.128  14.379
annotation-wrappers   6.484  0.136   7.027
* 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

* installing *source* package ‘AllelicImbalance’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing 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 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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, cbind, colMeans, colSums, colnames, 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


Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    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 
 13.512   0.272  14.327 

Example timings

AllelicImbalance.Rcheck/AllelicImbalance-Ex.timings

nameusersystemelapsed
ASEset-barplot0.3240.0160.339
ASEset-class0.6520.0040.655
ASEset-filters0.0760.0000.079
ASEset-gbarplot0.0240.0000.026
ASEset-glocationplot3.8680.0043.875
ASEset-gviztrack1.2480.0001.247
ASEset-scanForHeterozygotes1.7560.0241.784
ASEset.old0.0040.0000.000
ASEset.sim000
ASEsetFromBam0.0040.0000.002
DetectedAI-class0.0480.0000.049
DetectedAI-plot1.4760.0001.479
DetectedAI-summary0.0640.0040.069
GRvariants0.0000.0040.003
GlobalAnalysis-class0.0000.0040.003
LinkVariantAlmlof-class0.0000.0000.001
LinkVariantAlmlof-plot1.6520.0001.656
RegionSummary-class0.0000.0000.001
RiskVariant-class000
annotation-wrappers6.4840.1367.027
annotationBarplot000
barplot-lattice-support0.1120.0000.115
binom.test0.0240.0000.023
chisq.test0.0760.0000.075
cigar-utilities0.0080.0000.010
countAllelesFromBam0.0000.0000.002
coverageMatrixListFromGAL0.7560.0200.775
decorateWithExons0.0000.0000.002
decorateWithGenes0.0000.0000.003
defaultMapBias0.0640.0000.064
defaultPhase0.0000.0000.001
detectAI0.0360.0040.042
fractionPlotDf0.0200.0000.023
gba000
genomatrix000
genotype2phase0.0240.0040.030
getAlleleCounts3.5680.0043.580
getAlleleQuality4.0600.0004.065
getAreaFromGeneNames0.3920.0040.395
getDefaultMapBiasExpMean0.0240.0000.024
getSnpIdFromLocation18.372 0.96824.944
histplot0.0000.0000.001
implodeList-old0.0080.0000.005
import-bam-20.0080.0000.006
import-bam14.236 0.12814.379
import-bcf0.6440.0160.664
inferAlleles0.0600.0000.061
inferAltAllele0.0120.0000.011
inferGenotypes0.060.000.06
initialize-ASEset0.1640.0000.164
initialize-DetectedAI0.0480.0000.047
initialize-GlobalAnalysis0.0040.0000.004
initialize-RiskVariant0.0000.0000.001
legendBarplot0.0000.0000.001
locationplot1.3120.0001.314
lva4.9640.0004.971
lva.internal0.1840.0000.183
makeMaskedFasta0.6440.0000.645
mapBiasRef0.0120.0000.009
minCountFilt0.0280.0000.026
minFreqFilt0.0200.0040.026
multiAllelicFilt0.0080.0000.009
phase2genotype0.0160.0000.015
phaseArray2phaseMatrix0.0080.0000.007
phaseMatrix2Array0.0040.0040.006
randomRef0.0120.0000.011
reads0.0000.0000.001
refAllele0.0160.0000.012
regionSummary0.3360.0040.343
scanForHeterozygotes-old3.3880.0003.394